2-218661926-G-A

Variant names:

• chr2-218661926-G-A
• rs58447305
• NM_001079866.2:c.628G>A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:13
• Conservation: PhyloP100: 2.36
• Publications: 10 publications found

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

ACMG classification

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
BCS1L	NM_001079866.2	c.628G>A	p.Asp210Asn	missense_variant	Exon 4 of 8	ENST00000359273.8	NP_001073335.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCS1L	ENST00000359273.8	c.628G>A	p.Asp210Asn	missense_variant	Exon 4 of 8	1	NM_001079866.2	ENSP00000352219.3

Frequencies

GnomAD3 genomes AF: 0.0560 AC: 8519 AN: 152074 Hom.: 672 Cov.: 32

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

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

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

GnomAD4 genome AF: 0.0562 AC: 8552 AN: 152192 Hom.: 677 Cov.: 32 AF XY: 0.0536 AC XY: 3989 AN XY: 74418

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

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

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

Other links and lift over

dbSNP: rs58447305; hg19: chr2-219526649;