2-218661926-G-A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001079866.2(BCS1L):​c.628G>A​(p.Asp210Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0131 in 1,613,996 control chromosomes in the GnomAD database, including 1,415 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. D210D) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.056 ( 677 hom., cov: 32)
Exomes 𝑓: 0.0086 ( 738 hom. )

Consequence

BCS1L
NM_001079866.2 missense

Scores

3
15

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:13

Conservation

PhyloP100: 2.36

Publications

10 publications found
Variant links:
Genes affected
BCS1L (HGNC:1020): (BCS1 homolog, ubiquinol-cytochrome c reductase complex chaperone) This gene encodes a homolog of the S. cerevisiae bcs1 protein which is involved in the assembly of complex III of the mitochondrial respiratory chain. The encoded protein does not contain a mitochondrial targeting sequence but experimental studies confirm that it is imported into mitochondria. Mutations in this gene are associated with mitochondrial complex III deficiency and the GRACILE syndrome. Several alternatively spliced transcripts encoding two different isoforms have been described. [provided by RefSeq, Jan 2016]
BCS1L Gene-Disease associations (from GenCC):
  • Bjornstad syndrome
    Inheritance: AR, AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Orphanet, Ambry Genetics, ClinGen, G2P
  • GRACILE syndrome
    Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P
  • Leigh syndrome
    Inheritance: AR Classification: STRONG, LIMITED Submitted by: PanelApp Australia, ClinGen
  • mitochondrial complex III deficiency nuclear type 1
    Inheritance: AR Classification: STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
  • mitochondrial complex III deficiency
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • renal tubulopathy-encephalopathy-liver failure syndrome
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0016899705).
BP6
Variant 2-218661926-G-A is Benign according to our data. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218661926-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 136502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BCS1LNM_001079866.2 linkc.628G>A p.Asp210Asn missense_variant Exon 4 of 8 ENST00000359273.8 NP_001073335.1 Q9Y276A0A024R445

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BCS1LENST00000359273.8 linkc.628G>A p.Asp210Asn missense_variant Exon 4 of 8 1 NM_001079866.2 ENSP00000352219.3 Q9Y276

Frequencies

GnomAD3 genomes
AF:
0.0560
AC:
8519
AN:
152074
Hom.:
672
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.185
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0276
Gnomad ASJ
AF:
0.0156
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00849
Gnomad FIN
AF:
0.000377
Gnomad MID
AF:
0.0538
Gnomad NFE
AF:
0.00350
Gnomad OTH
AF:
0.0480
GnomAD2 exomes
AF:
0.0182
AC:
4579
AN:
251114
AF XY:
0.0146
show subpopulations
Gnomad AFR exome
AF:
0.195
Gnomad AMR exome
AF:
0.0150
Gnomad ASJ exome
AF:
0.0146
Gnomad EAS exome
AF:
0.0000544
Gnomad FIN exome
AF:
0.000185
Gnomad NFE exome
AF:
0.00378
Gnomad OTH exome
AF:
0.0189
GnomAD4 exome
AF:
0.00864
AC:
12634
AN:
1461804
Hom.:
738
Cov.:
33
AF XY:
0.00811
AC XY:
5900
AN XY:
727196
show subpopulations
African (AFR)
AF:
0.200
AC:
6684
AN:
33474
American (AMR)
AF:
0.0156
AC:
697
AN:
44712
Ashkenazi Jewish (ASJ)
AF:
0.0166
AC:
434
AN:
26126
East Asian (EAS)
AF:
0.0000252
AC:
1
AN:
39700
South Asian (SAS)
AF:
0.00723
AC:
623
AN:
86226
European-Finnish (FIN)
AF:
0.000262
AC:
14
AN:
53408
Middle Eastern (MID)
AF:
0.0347
AC:
200
AN:
5768
European-Non Finnish (NFE)
AF:
0.00254
AC:
2823
AN:
1111994
Other (OTH)
AF:
0.0192
AC:
1158
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.478
Heterozygous variant carriers
0
709
1418
2126
2835
3544
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
266
532
798
1064
1330
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.0562
AC:
8552
AN:
152192
Hom.:
677
Cov.:
32
AF XY:
0.0536
AC XY:
3989
AN XY:
74418
show subpopulations
African (AFR)
AF:
0.185
AC:
7671
AN:
41490
American (AMR)
AF:
0.0276
AC:
422
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.0156
AC:
54
AN:
3470
East Asian (EAS)
AF:
0.000193
AC:
1
AN:
5176
South Asian (SAS)
AF:
0.00891
AC:
43
AN:
4826
European-Finnish (FIN)
AF:
0.000377
AC:
4
AN:
10616
Middle Eastern (MID)
AF:
0.0612
AC:
18
AN:
294
European-Non Finnish (NFE)
AF:
0.00350
AC:
238
AN:
68018
Other (OTH)
AF:
0.0480
AC:
101
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
383
766
1150
1533
1916
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
86
172
258
344
430
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0203
Hom.:
524
Bravo
AF:
0.0641
TwinsUK
AF:
0.00135
AC:
5
ALSPAC
AF:
0.00182
AC:
7
ESP6500AA
AF:
0.182
AC:
803
ESP6500EA
AF:
0.00488
AC:
42
ExAC
AF:
0.0214
AC:
2603
Asia WGS
AF:
0.0160
AC:
57
AN:
3478
EpiCase
AF:
0.00551
EpiControl
AF:
0.00563

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:13
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:4
Nov 09, 2018
Athena Diagnostics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

-
Breakthrough Genomics, Breakthrough Genomics
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:not provided

- -

Feb 03, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Mar 15, 2016
Mayo Clinic Laboratories, Mayo Clinic
Significance:Benign
Review Status:no assertion criteria provided
Collection Method:clinical testing

- -

GRACILE syndrome Benign:3
Sep 16, 2020
Natera, Inc.
Significance:Benign
Review Status:no assertion criteria provided
Collection Method:clinical testing

- -

Jun 10, 2021
Genome-Nilou Lab
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Apr 27, 2017
Illumina Laboratory Services, Illumina
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

not specified Benign:2
Mar 21, 2016
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

p.Asp210Asn in exon 5 of BCS1L: This variant is not expected to have clinical si gnificance because it has been identified in 23.75% (314/1322) of African chromo somes by the 1000 Genomes Project (Phase 3; dbSNP rs58447305). -

Dec 09, 2011
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Mitochondrial complex III deficiency nuclear type 1 Benign:2
Jun 10, 2021
Genome-Nilou Lab
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Apr 27, 2017
Illumina Laboratory Services, Illumina
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

Leigh syndrome Benign:1
Apr 27, 2017
Illumina Laboratory Services, Illumina
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

Pili torti-deafness syndrome Benign:1
Jun 10, 2021
Genome-Nilou Lab
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.068
BayesDel_addAF
Benign
-0.55
T
BayesDel_noAF
Benign
-0.42
CADD
Benign
21
DANN
Benign
0.93
DEOGEN2
Benign
0.13
.;T;T;T;T;T;T;T
Eigen
Benign
-0.30
Eigen_PC
Benign
-0.027
FATHMM_MKL
Uncertain
0.81
D
LIST_S2
Uncertain
0.87
D;.;.;.;.;.;.;D
MetaRNN
Benign
0.0017
T;T;T;T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.54
.;N;N;N;N;N;N;N
PhyloP100
2.4
PrimateAI
Benign
0.31
T
PROVEAN
Benign
0.73
N;N;N;N;N;N;N;N
REVEL
Uncertain
0.33
Sift
Benign
0.63
T;T;T;T;T;T;T;T
Sift4G
Benign
0.59
T;T;T;T;T;T;T;T
Polyphen
0.0020
.;B;B;B;B;B;B;B
Vest4
0.12, 0.13, 0.078, 0.077, 0.076
MPC
0.59
ClinPred
0.013
T
GERP RS
4.8
PromoterAI
-0.045
Neutral
Varity_R
0.11
gMVP
0.54
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs58447305; hg19: chr2-219526649; API