Variant 13-102839742-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_017693.4(BIVM):c.1389G>A(p.Gly463=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00932 in 1,614,194 control chromosomes in the GnomAD database, including 123 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0066 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0096 ( 120 hom. )

Consequence

BIVM
NM_017693.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.29

Variant links:

Genes affected

BIVM (HGNC:16034): (basic, immunoglobulin-like variable motif containing) Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

BIVM links:

BIVM-ERCC5 (HGNC:):

BIVM-ERCC5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 13-102839742-G-A is Benign according to our data. Variant chr13-102839742-G-A is described in ClinVar as [Benign]. Clinvar id is 783043.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.29 with no splicing effect.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00659 (1003/152302) while in subpopulation SAS AF= 0.0205 (99/4826). AF 95% confidence interval is 0.0172. There are 3 homozygotes in gnomad4. There are 496 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
BIVM	NM_017693.4 linkuse as main transcript	c.1389G>A	p.Gly463=	synonymous_variant	11/11	ENST00000257336.6
BIVM-ERCC5	NM_001204425.2 linkuse as main transcript	c.1389G>A	p.Gly463=	synonymous_variant	9/23
BIVM	NM_001159596.2 linkuse as main transcript	c.723G>A	p.Gly241=	synonymous_variant	9/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BIVM	ENST00000257336.6 linkuse as main transcript	c.1389G>A	p.Gly463=	synonymous_variant	11/11	1	NM_017693.4	P1	Q86UB2-1

Frequencies

GnomAD3 genomes

AF:

0.00659

AC:

1003

AN:

152184

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00171

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00550

Gnomad ASJ

AF:

0.0127

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0203

Gnomad FIN

AF:

0.00406

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00946

Gnomad OTH

AF:

0.00525

GnomAD3 exomes

AF:

0.00849

AC:

2133

AN:

251364

Hom.:

AF XY:

0.00944

AC XY:

1283

AN XY:

135850

show subpopulations

Gnomad AFR exome

AF:

0.00154

Gnomad AMR exome

AF:

0.00474

Gnomad ASJ exome

AF:

0.0104

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0250

Gnomad FIN exome

AF:

0.00328

Gnomad NFE exome

AF:

0.00826

Gnomad OTH exome

AF:

0.0104

GnomAD4 exome

AF:

0.00961

AC:

14049

AN:

1461892

Hom.:

120

Cov.:

AF XY:

0.0102

AC XY:

7399

AN XY:

727248

show subpopulations

Gnomad4 AFR exome

AF:

0.00131

Gnomad4 AMR exome

AF:

0.00472

Gnomad4 ASJ exome

AF:

0.0109

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0249

Gnomad4 FIN exome

AF:

0.00313

Gnomad4 NFE exome

AF:

0.00943

Gnomad4 OTH exome

AF:

0.0105

GnomAD4 genome

AF:

0.00659

AC:

1003

AN:

152302

Hom.:

Cov.:

AF XY:

0.00666

AC XY:

496

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.00171

Gnomad4 AMR

AF:

0.00549

Gnomad4 ASJ

AF:

0.0127

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0205

Gnomad4 FIN

AF:

0.00406

Gnomad4 NFE

AF:

0.00947

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00860

Hom.:

Bravo

AF:

0.00615

Asia WGS

AF:

0.00635

AC:

AN:

3478

EpiCase

AF:

0.00927

EpiControl

AF:

0.00794

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Nov 20, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

6.5

DANN

Benign

0.62

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

LitVar

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over