Variant 6-26388177-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_006995.5(BTN2A2):c.607G>A(p.Gly203Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.05 in 1,614,116 control chromosomes in the GnomAD database, including 2,256 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.052 ( 221 hom., cov: 32)

Exomes 𝑓: 0.050 ( 2035 hom. )

Consequence

BTN2A2
NM_006995.5 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 3.19

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:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0036383271).

BP6

Variant 6-26388177-G-A is Benign according to our data. Variant chr6-26388177-G-A is described in ClinVar as [Benign]. Clinvar id is 3057059.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0564 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.607G>A	p.Gly203Ser	missense_variant	4/8	ENST00000356709.9	NP_008926.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTN2A2	ENST00000356709.9 linkuse as main transcript	c.607G>A	p.Gly203Ser	missense_variant	4/8	1	NM_006995.5	ENSP00000349143	P1	Q8WVV5-1
	ENST00000707189.1 linkuse as main transcript	n.1000-165010G>A		intron_variant, non_coding_transcript_variant
	ENST00000707191.1 linkuse as main transcript	n.1001-144528G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0520

AC:

7916

AN:

152108

Hom.:

223

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0584

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.0569

Gnomad ASJ

AF:

0.0929

Gnomad EAS

AF:

0.00442

Gnomad SAS

AF:

0.0573

Gnomad FIN

AF:

0.0141

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0545

Gnomad OTH

AF:

0.0546

GnomAD3 exomes

AF:

0.0476

AC:

11979

AN:

251476

Hom.:

358

AF XY:

0.0495

AC XY:

6731

AN XY:

135906

show subpopulations

Gnomad AFR exome

AF:

0.0593

Gnomad AMR exome

AF:

0.0367

Gnomad ASJ exome

AF:

0.100

Gnomad EAS exome

AF:

0.00239

Gnomad SAS exome

AF:

0.0620

Gnomad FIN exome

AF:

0.0160

Gnomad NFE exome

AF:

0.0534

Gnomad OTH exome

AF:

0.0598

GnomAD4 exome

AF:

0.0498

AC:

72819

AN:

1461892

Hom.:

2035

Cov.:

AF XY:

0.0509

AC XY:

36984

AN XY:

727248

show subpopulations

Gnomad4 AFR exome

AF:

0.0619

Gnomad4 AMR exome

AF:

0.0402

Gnomad4 ASJ exome

AF:

0.101

Gnomad4 EAS exome

AF:

0.00189

Gnomad4 SAS exome

AF:

0.0630

Gnomad4 FIN exome

AF:

0.0153

Gnomad4 NFE exome

AF:

0.0506

Gnomad4 OTH exome

AF:

0.0543

GnomAD4 genome

AF:

0.0520

AC:

7913

AN:

152224

Hom.:

221

Cov.:

AF XY:

0.0504

AC XY:

3752

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.0584

Gnomad4 AMR

AF:

0.0568

Gnomad4 ASJ

AF:

0.0929

Gnomad4 EAS

AF:

0.00443

Gnomad4 SAS

AF:

0.0568

Gnomad4 FIN

AF:

0.0141

Gnomad4 NFE

AF:

0.0545

Gnomad4 OTH

AF:

0.0541

Alfa

AF:

0.0492

Hom.:

150

Bravo

AF:

0.0558

TwinsUK

AF:

0.0515

AC:

191

ALSPAC

AF:

0.0498

AC:

192

ESP6500AA

AF:

0.0617

AC:

272

ESP6500EA

AF:

0.0562

AC:

483

ExAC

AF:

0.0484

AC:

5875

Asia WGS

AF:

0.0410

AC:

141

AN:

3478

EpiCase

AF:

0.0625

EpiControl

AF:

0.0609

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 06, 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

AlphaMissense

Benign

0.082

BayesDel_addAF

Benign

-0.46

BayesDel_noAF

Benign

-0.39

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.13

.;T;.;.;.;T;.

Eigen

Benign

0.080

Eigen_PC

Benign

-0.057

FATHMM_MKL

Benign

0.45

LIST_S2

Benign

0.75

T;.;T;T;T;T;T

MetaRNN

Benign

0.0036

T;T;T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.5

M;M;.;.;.;M;.

MutationTaster

Benign

0.60

P;P;P;P;P;P

PrimateAI

Benign

0.37

PROVEAN

Pathogenic

-5.4

D;D;D;D;D;D;D

REVEL

Benign

0.20

Sift

Benign

0.044

D;D;D;D;D;D;D

Sift4G

Benign

0.061

T;D;T;T;T;D;T

Polyphen

0.98

D;P;.;.;.;P;.

Vest4

0.19

MPC

0.44

ClinPred

0.071

GERP RS

3.2

Varity_R

0.29

gMVP

0.44

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.11

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