Variant chr13-102807511-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_017693.4(BIVM):c.244A>G(p.Ile82Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00808 in 1,614,190 control chromosomes in the GnomAD database, including 72 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0057 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0083 ( 70 hom. )

Consequence

BIVM
NM_017693.4 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.157

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 -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0057371855).

BP6

Variant 13-102807511-A-G is Benign according to our data. Variant chr13-102807511-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1686561.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
BIVM	NM_017693.4 linkuse as main transcript	c.244A>G	p.Ile82Val	missense_variant	3/11	ENST00000257336.6
BIVM-ERCC5	NM_001204425.2 linkuse as main transcript	c.244A>G	p.Ile82Val	missense_variant	1/23
BIVM	NM_001159596.2 linkuse as main transcript	c.-210+7990A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BIVM	ENST00000257336.6 linkuse as main transcript	c.244A>G	p.Ile82Val	missense_variant	3/11	1	NM_017693.4	P1	Q86UB2-1

Frequencies

GnomAD3 genomes

AF:

0.00567

AC:

863

AN:

152184

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00159

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.00255

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00290

Gnomad FIN

AF:

0.00301

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0101

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.00551

AC:

1386

AN:

251474

Hom.:

AF XY:

0.00561

AC XY:

763

AN XY:

135912

show subpopulations

Gnomad AFR exome

AF:

0.00166

Gnomad AMR exome

AF:

0.00208

Gnomad ASJ exome

AF:

0.00317

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00193

Gnomad FIN exome

AF:

0.00203

Gnomad NFE exome

AF:

0.00985

Gnomad OTH exome

AF:

0.00505

GnomAD4 exome

AF:

0.00834

AC:

12185

AN:

1461888

Hom.:

Cov.:

AF XY:

0.00816

AC XY:

5933

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.00158

Gnomad4 AMR exome

AF:

0.00244

Gnomad4 ASJ exome

AF:

0.00356

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00236

Gnomad4 FIN exome

AF:

0.00256

Gnomad4 NFE exome

AF:

0.0101

Gnomad4 OTH exome

AF:

0.00608

GnomAD4 genome

AF:

0.00567

AC:

863

AN:

152302

Hom.:

Cov.:

AF XY:

0.00518

AC XY:

386

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.00159

Gnomad4 AMR

AF:

0.00255

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00290

Gnomad4 FIN

AF:

0.00301

Gnomad4 NFE

AF:

0.0101

Gnomad4 OTH

AF:

0.00520

Alfa

AF:

0.00844

Hom.:

Bravo

AF:

0.00520

TwinsUK

AF:

0.00809

AC:

ALSPAC

AF:

0.00830

AC:

ESP6500AA

AF:

0.00227

AC:

ESP6500EA

AF:

0.0115

AC:

ExAC

AF:

0.00544

AC:

661

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2024	BIVM: BP4, BS2 -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Mendelics

May 04, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.063

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.57

CADD

Benign

3.4

DANN

Benign

0.58

DEOGEN2

Benign

0.011

T;.;.

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.17

LIST_S2

Benign

0.62

T;T;.

MetaRNN

Benign

0.0057

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.26

N;.;.

MutationTaster

Benign

1.0

D;N;N

PROVEAN

Benign

-0.030

N;.;.

REVEL

Benign

0.018

Sift

Benign

0.73

T;.;.

Sift4G

Benign

0.91

T;.;.

Polyphen

0.0

B;.;.

Vest4

0.064

MVP

0.081

MPC

0.23

ClinPred

0.00031

GERP RS

-1.0

Varity_R

0.013

gMVP

0.14

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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