Variant rs13195509 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007049.5(BTN2A1):c.619G>A(p.Val207Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0907 in 1,613,960 control chromosomes in the GnomAD database, including 8,099 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.063 ( 390 hom., cov: 31)

Exomes 𝑓: 0.094 ( 7709 hom. )

Consequence

BTN2A1
NM_007049.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0610

Variant links:

Genes affected

BTN2A1 (HGNC:1136): (butyrophilin subfamily 2 member A1) This gene encodes a member of the immunoglobulin superfamily. The gene is located in a cluster of butyrophilin-like genes in the juxta-telomeric region of the major histocompatibility complex on chromosome 6. A pseudogene of this gene has been identified in this cluster. The encoded protein is an integral plasma membrane protein involved in lipid, fatty-acid, and sterol metabolism. Alterations in this gene may be associated with several disease states including metabolic syndrome. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2013]

BTN2A1 links:

ENSG00000291336 (HGNC:):

ENSG00000291336 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017808676).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTN2A1	NM_007049.5 link	c.619G>A	p.Val207Met	missense_variant	4/8	ENST00000312541.10	NP_008980.1	Q7KYR7-2
BTN2A1	NM_001197233.3 link	c.436G>A	p.Val146Met	missense_variant	3/7		NP_001184162.1	Q7KYR7-5
BTN2A1	NM_078476.4 link	c.619G>A	p.Val207Met	missense_variant	4/8		NP_510961.1	Q7KYR7-4
BTN2A1	NM_001197234.3 link	c.619G>A	p.Val207Met	missense_variant	4/8		NP_001184163.1	Q7KYR7-6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTN2A1	ENST00000312541.10 link	c.619G>A	p.Val207Met	missense_variant	4/8	1	NM_007049.5	ENSP00000312158.5		Q7KYR7-2

Frequencies

GnomAD3 genomes

AF:

0.0629

AC:

9574

AN:

152112

Hom.:

390

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0412

Gnomad AMI

AF:

0.186

Gnomad AMR

AF:

0.0329

Gnomad ASJ

AF:

0.0202

Gnomad EAS

AF:

0.00617

Gnomad SAS

AF:

0.0234

Gnomad FIN

AF:

0.0452

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0941

Gnomad OTH

AF:

0.0459

GnomAD3 exomes

AF:

0.0568

AC:

14278

AN:

251410

Hom.:

612

AF XY:

0.0575

AC XY:

7811

AN XY:

135870

show subpopulations

Gnomad AFR exome

AF:

0.0407

Gnomad AMR exome

AF:

0.0223

Gnomad ASJ exome

AF:

0.0197

Gnomad EAS exome

AF:

0.00560

Gnomad SAS exome

AF:

0.0281

Gnomad FIN exome

AF:

0.0490

Gnomad NFE exome

AF:

0.0907

Gnomad OTH exome

AF:

0.0509

GnomAD4 exome

AF:

0.0936

AC:

136824

AN:

1461730

Hom.:

7709

Cov.:

AF XY:

0.0909

AC XY:

66114

AN XY:

727152

show subpopulations

Gnomad4 AFR exome

AF:

0.0422

Gnomad4 AMR exome

AF:

0.0228

Gnomad4 ASJ exome

AF:

0.0208

Gnomad4 EAS exome

AF:

0.0220

Gnomad4 SAS exome

AF:

0.0288

Gnomad4 FIN exome

AF:

0.0500

Gnomad4 NFE exome

AF:

0.111

Gnomad4 OTH exome

AF:

0.0765

GnomAD4 genome

AF:

0.0629

AC:

9572

AN:

152230

Hom.:

390

Cov.:

AF XY:

0.0583

AC XY:

4340

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.0411

Gnomad4 AMR

AF:

0.0329

Gnomad4 ASJ

AF:

0.0202

Gnomad4 EAS

AF:

0.00618

Gnomad4 SAS

AF:

0.0233

Gnomad4 FIN

AF:

0.0452

Gnomad4 NFE

AF:

0.0941

Gnomad4 OTH

AF:

0.0455

Alfa

AF:

0.0806

Hom.:

1469

Bravo

AF:

0.0610

TwinsUK

AF:

0.133

AC:

495

ALSPAC

AF:

0.123

AC:

473

ESP6500AA

AF:

0.0427

AC:

188

ESP6500EA

AF:

0.0924

AC:

795

ExAC

AF:

0.0585

AC:

7098

Asia WGS

AF:

0.0180

AC:

AN:

3478

EpiCase

AF:

0.0858

EpiControl

AF:

0.0821

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.50

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0051

.;T;.;.

Eigen

Benign

0.063

Eigen_PC

Benign

-0.15

FATHMM_MKL

Benign

0.099

LIST_S2

Uncertain

0.87

D;D;D;D

MetaRNN

Benign

0.0018

T;T;T;T

MetaSVM

Benign

-0.42

MutationAssessor

Uncertain

2.7

.;M;M;M

PrimateAI

Benign

0.42

PROVEAN

Benign

-1.9

N;N;N;N

REVEL

Benign

0.22

Sift

Benign

0.078

T;T;T;T

Sift4G

Benign

0.11

T;T;D;D

Polyphen

1.0

.;D;.;.

Vest4

0.10

MPC

0.28

ClinPred

0.028

GERP RS

2.0

Varity_R

0.056

gMVP

0.096

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over