dbSNP rs12176317: BTN3A2:c.716-339A>G (chr6-26372558-A-G) – 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.716-339A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0829 in 255,654 control chromosomes in the GnomAD database, including 1,101 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: 32)

Exomes 𝑓: 0.093 ( 546 hom. )

Consequence

BTN3A2
NM_007047.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0630

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=-0.94).

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.716-339A>G		intron_variant	Intron 5 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.716-339A>G		intron_variant	Intron 5 of 10	1	NM_007047.5	ENSP00000366937.2		P78410-1

Frequencies

GnomAD3 genomes

AF:

0.0764

AC:

11621

AN:

152156

Hom.:

556

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0340

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.0400

Gnomad ASJ

AF:

0.0297

Gnomad EAS

AF:

0.0861

Gnomad SAS

AF:

0.0980

Gnomad FIN

AF:

0.0709

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.0686

GnomAD4 exome

AF:

0.0927

AC:

9587

AN:

103380

Hom.:

546

AF XY:

0.0931

AC XY:

5060

AN XY:

54322

show subpopulations

African (AFR)

AF:

0.0346

AC:

113

AN:

3264

American (AMR)

AF:

0.0370

AC:

175

AN:

4724

Ashkenazi Jewish (ASJ)

AF:

0.0331

AC:

AN:

2780

East Asian (EAS)

AF:

0.0803

AC:

397

AN:

4942

South Asian (SAS)

AF:

0.0921

AC:

1319

AN:

14316

European-Finnish (FIN)

AF:

0.0918

AC:

419

AN:

4566

Middle Eastern (MID)

AF:

0.0556

AC:

AN:

432

European-Non Finnish (NFE)

AF:

0.105

AC:

6571

AN:

62748

Other (OTH)

AF:

0.0851

AC:

477

AN:

5608

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

409

818

1227

1636

2045

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

116

174

232

290

<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:

11612

AN:

152274

Hom.:

555

Cov.:

AF XY:

0.0732

AC XY:

5453

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.0340

AC:

1414

AN:

41566

American (AMR)

AF:

0.0398

AC:

609

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0297

AC:

103

AN:

3470

East Asian (EAS)

AF:

0.0863

AC:

448

AN:

5192

South Asian (SAS)

AF:

0.0968

AC:

467

AN:

4824

European-Finnish (FIN)

AF:

0.0709

AC:

752

AN:

10600

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.110

AC:

7486

AN:

68014

Other (OTH)

AF:

0.0688

AC:

145

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

550

1100

1650

2200

2750

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

280

420

560

700

<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:

0.0982

Hom.:

2606

Bravo

AF:

0.0712

Asia WGS

AF:

0.0990

AC:

343

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

4.7

(source)

DANN

Benign

0.57

PhyloP100

-0.063

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