Genetic Variant BTN3A2:c.964+37G>A (chr6-26373450-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007047.5(BTN3A2):c.964+37G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 1,590,080 control chromosomes in the GnomAD database, including 10,453 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.076 ( 555 hom., cov: 27)

Exomes 𝑓: 0.11 ( 9898 hom. )

Consequence

BTN3A2
NM_007047.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.83

Publications

35 publications found

Variant links:

Genes affected

BTN3A2 (HGNC:1139): (butyrophilin subfamily 3 member A2) This gene encodes a member of the immunoglobulin superfamily, which resides in the juxta-telomeric region of the major histocompatability class 1 locus and is clustered with the other family members on chromosome 6. The encoded protein may be involved in the adaptive immune response. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2013]

BTN3A2 links:

ENSG00000291336 (HGNC:):

ENSG00000291336 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.03).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTN3A2	NM_007047.5 link	c.964+37G>A		intron_variant	Intron 8 of 10	ENST00000377708.7	NP_008978.2	P78410-1A8K4B5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTN3A2	ENST00000377708.7 link	c.964+37G>A		intron_variant	Intron 8 of 10	1	NM_007047.5	ENSP00000366937.2		P78410-1

Frequencies

GnomAD3 genomes

AF:

0.0764

AC:

11574

AN:

151454

Hom.:

556

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0341

Gnomad AMI

AF:

0.190

Gnomad AMR

AF:

0.0401

Gnomad ASJ

AF:

0.0297

Gnomad EAS

AF:

0.0860

Gnomad SAS

AF:

0.0978

Gnomad FIN

AF:

0.0706

Gnomad MID

AF:

0.0541

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.0676

GnomAD2 exomes

AF:

0.0826

AC:

19035

AN:

230524

AF XY:

0.0854

show subpopulations

Gnomad AFR exome

AF:

0.0352

Gnomad AMR exome

AF:

0.0323

Gnomad ASJ exome

AF:

0.0325

Gnomad EAS exome

AF:

0.0838

Gnomad FIN exome

AF:

0.0764

Gnomad NFE exome

AF:

0.107

Gnomad OTH exome

AF:

0.0724

GnomAD4 exome

AF:

0.111

AC:

160368

AN:

1438508

Hom.:

9898

Cov.:

AF XY:

0.110

AC XY:

79001

AN XY:

715234

show subpopulations

African (AFR)

AF:

0.0337

AC:

1083

AN:

32100

American (AMR)

AF:

0.0318

AC:

1248

AN:

39228

Ashkenazi Jewish (ASJ)

AF:

0.0331

AC:

829

AN:

25046

East Asian (EAS)

AF:

0.0910

AC:

3602

AN:

39568

South Asian (SAS)

AF:

0.0885

AC:

7196

AN:

81304

European-Finnish (FIN)

AF:

0.0765

AC:

4059

AN:

53026

Middle Eastern (MID)

AF:

0.0532

AC:

301

AN:

5662

European-Non Finnish (NFE)

AF:

0.124

AC:

136322

AN:

1103202

Other (OTH)

AF:

0.0965

AC:

5728

AN:

59372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.456

Heterozygous variant carriers

6414

12828

19242

25656

32070

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5052

10104

15156

20208

25260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0763

AC:

11565

AN:

151572

Hom.:

555

Cov.:

AF XY:

0.0732

AC XY:

5422

AN XY:

74048

show subpopulations

African (AFR)

AF:

0.0341

AC:

1410

AN:

41380

American (AMR)

AF:

0.0400

AC:

609

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.0297

AC:

103

AN:

3468

East Asian (EAS)

AF:

0.0862

AC:

445

AN:

5164

South Asian (SAS)

AF:

0.0966

AC:

463

AN:

4792

European-Finnish (FIN)

AF:

0.0706

AC:

732

AN:

10364

Middle Eastern (MID)

AF:

0.0479

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.110

AC:

7474

AN:

67864

Other (OTH)

AF:

0.0678

AC:

142

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

539

1079

1618

2158

2697

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0971

Hom.:

2440

Bravo

AF:

0.0712

Asia WGS

AF:

0.0990

AC:

345

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.18

(source)

DANN

Benign

0.60

PhyloP100

-1.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over