Variant chr6-26392287-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_001197240.2(BTN2A2):c.763G>C(p.Ala255Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,601,016 control chromosomes in the GnomAD database, including 11,142 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.078 ( 585 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10557 hom. )

Consequence

BTN2A2
NM_001197240.2 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.580

Variant links:

Genes affected

BTN2A2 (HGNC:1137): (butyrophilin subfamily 2 member A2) Butyrophilin is the major protein associated with fat droplets in the milk. This gene is a member of the BTN2 subfamily of genes, which encode proteins belonging to the butyrophilin protein family. The gene is located in a cluster on chromosome 6, consisting of seven genes belonging to the expanding B7/butyrophilin-like group, a subset of the immunoglobulin gene superfamily. The encoded protein is a type I receptor glycoprotein involved in lipid, fatty-acid and sterol metabolism. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2010]

BTN2A2 links:

ENSG00000291336 (HGNC:):

ENSG00000291336 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0015104413).

BP6

Variant 6-26392287-G-C is Benign according to our data. Variant chr6-26392287-G-C is described in ClinVar as [Benign]. Clinvar id is 3059309.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTN2A2	NM_006995.5 linkuse as main transcript	c.980-88G>C		intron_variant		ENST00000356709.9	NP_008926.2	Q8WVV5-1A0A024R038

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTN2A2	ENST00000356709.9 linkuse as main transcript	c.980-88G>C		intron_variant		1	NM_006995.5	ENSP00000349143.4		Q8WVV5-1

Frequencies

GnomAD3 genomes

AF:

0.0785

AC:

11948

AN:

152140

Hom.:

587

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0337

Gnomad AMI

AF:

0.200

Gnomad AMR

AF:

0.0393

Gnomad ASJ

AF:

0.0415

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.0782

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.0651

GnomAD3 exomes

AF:

0.0855

AC:

19218

AN:

224716

Hom.:

963

AF XY:

0.0885

AC XY:

10788

AN XY:

121840

show subpopulations

Gnomad AFR exome

AF:

0.0346

Gnomad AMR exome

AF:

0.0326

Gnomad ASJ exome

AF:

0.0419

Gnomad EAS exome

AF:

0.0955

Gnomad SAS exome

AF:

0.0925

Gnomad FIN exome

AF:

0.0856

Gnomad NFE exome

AF:

0.111

Gnomad OTH exome

AF:

0.0759

GnomAD4 exome

AF:

0.115

AC:

166972

AN:

1448758

Hom.:

10557

Cov.:

AF XY:

0.114

AC XY:

82158

AN XY:

719436

show subpopulations

Gnomad4 AFR exome

AF:

0.0352

Gnomad4 AMR exome

AF:

0.0324

Gnomad4 ASJ exome

AF:

0.0446

Gnomad4 EAS exome

AF:

0.132

Gnomad4 SAS exome

AF:

0.0912

Gnomad4 FIN exome

AF:

0.0834

Gnomad4 NFE exome

AF:

0.126

Gnomad4 OTH exome

AF:

0.0994

GnomAD4 genome

AF:

0.0784

AC:

11939

AN:

152258

Hom.:

585

Cov.:

AF XY:

0.0757

AC XY:

5632

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.0337

Gnomad4 AMR

AF:

0.0391

Gnomad4 ASJ

AF:

0.0415

Gnomad4 EAS

AF:

0.102

Gnomad4 SAS

AF:

0.100

Gnomad4 FIN

AF:

0.0782

Gnomad4 NFE

AF:

0.112

Gnomad4 OTH

AF:

0.0654

Alfa

AF:

0.106

Hom.:

553

Bravo

AF:

0.0731

TwinsUK

AF:

0.149

AC:

552

ALSPAC

AF:

0.138

AC:

531

ExAC

AF:

0.0825

AC:

9981

Asia WGS

AF:

0.102

AC:

355

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

BTN2A2-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 04, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.40

CADD

Benign

3.9

DANN

Benign

0.46

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.037

LIST_S2

Benign

0.27

MetaRNN

Benign

0.0015

MetaSVM

Benign

-0.83

PROVEAN

Benign

-0.63

REVEL

Benign

0.13

Sift

Pathogenic

0.0

Vest4

0.061

ClinPred

0.010

GERP RS

-2.8

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