10-102854363-C-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_001136200.2(BORCS7):​c.77C>A​(p.Thr26Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000171 in 1,581,186 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000018 ( 0 hom. )

Consequence

BORCS7
NM_001136200.2 missense

Scores

16

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.90
Variant links:
Genes affected
BORCS7 (HGNC:23516): (BLOC-1 related complex subunit 7) Part of BORC complex. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.065603614).
BP6
Variant 10-102854363-C-A is Benign according to our data. Variant chr10-102854363-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2290258.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BORCS7NM_001136200.2 linkuse as main transcriptc.77C>A p.Thr26Asn missense_variant 1/5 ENST00000339834.10
BORCS7-ASMTNR_037644.1 linkuse as main transcriptn.154C>A non_coding_transcript_exon_variant 1/15
BORCS7NM_144591.5 linkuse as main transcriptc.77C>A p.Thr26Asn missense_variant 1/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BORCS7ENST00000339834.10 linkuse as main transcriptc.77C>A p.Thr26Asn missense_variant 1/51 NM_001136200.2 P1
ENST00000631443.1 linkuse as main transcriptn.151G>T non_coding_transcript_exon_variant 1/34

Frequencies

GnomAD3 genomes
AF:
0.00000658
AC:
1
AN:
152058
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000153
AC:
3
AN:
196164
Hom.:
0
AF XY:
0.00000958
AC XY:
1
AN XY:
104406
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000669
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000239
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000182
AC:
26
AN:
1429128
Hom.:
0
Cov.:
30
AF XY:
0.0000113
AC XY:
8
AN XY:
707630
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000196
Gnomad4 NFE exome
AF:
0.0000210
Gnomad4 OTH exome
AF:
0.0000337
GnomAD4 genome
AF:
0.00000658
AC:
1
AN:
152058
Hom.:
0
Cov.:
31
AF XY:
0.0000135
AC XY:
1
AN XY:
74260
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000113

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Likely benign, criteria provided, single submitterclinical testingAmbry GeneticsMay 18, 2022This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.044
BayesDel_addAF
Benign
-0.28
T
BayesDel_noAF
Benign
-0.64
CADD
Benign
18
DANN
Benign
0.88
Eigen
Benign
-0.71
Eigen_PC
Benign
-0.46
FATHMM_MKL
Benign
0.37
N
LIST_S2
Benign
0.64
.;T
M_CAP
Benign
0.0029
T
MetaRNN
Benign
0.066
T;T
MetaSVM
Benign
-1.0
T
MutationTaster
Benign
0.77
D;D
PROVEAN
Benign
2.0
N;N
REVEL
Benign
0.10
Sift
Benign
0.80
T;T
Sift4G
Benign
1.0
T;T
Vest4
0.14
MVP
0.16
MPC
0.19
ClinPred
0.056
T
GERP RS
3.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
gMVP
0.30

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1295973025; hg19: chr10-104614120; API