Genetic Variant BTN3A2:c.*7-96A>G (chr6-26374675-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.*7-96A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 1,326,676 control chromosomes in the GnomAD database, including 50,699 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 0.28 ( 6372 hom., cov: 30)

Exomes 𝑓: 0.27 ( 44327 hom. )

Consequence

BTN3A2
NM_007047.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.261

Publications

10 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTN3A2	NM_007047.5 link	c.*7-96A>G		intron_variant	Intron 9 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.*7-96A>G		intron_variant	Intron 9 of 10	1	NM_007047.5	ENSP00000366937.2		P78410-1

Frequencies

GnomAD3 genomes

AF:

0.283

AC:

42990

AN:

151862

Hom.:

6364

Cov.:

show subpopulations

Gnomad AFR

AF:

0.334

Gnomad AMI

AF:

0.360

Gnomad AMR

AF:

0.239

Gnomad ASJ

AF:

0.244

Gnomad EAS

AF:

0.117

Gnomad SAS

AF:

0.311

Gnomad FIN

AF:

0.216

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.285

Gnomad OTH

AF:

0.265

GnomAD4 exome

AF:

0.271

AC:

318162

AN:

1174696

Hom.:

44327

Cov.:

AF XY:

0.272

AC XY:

161136

AN XY:

592378

show subpopulations

African (AFR)

AF:

0.336

AC:

9019

AN:

26850

American (AMR)

AF:

0.246

AC:

8711

AN:

35396

Ashkenazi Jewish (ASJ)

AF:

0.249

AC:

5186

AN:

20786

East Asian (EAS)

AF:

0.105

AC:

4024

AN:

38256

South Asian (SAS)

AF:

0.301

AC:

21555

AN:

71506

European-Finnish (FIN)

AF:

0.223

AC:

11239

AN:

50316

Middle Eastern (MID)

AF:

0.239

AC:

876

AN:

3664

European-Non Finnish (NFE)

AF:

0.278

AC:

244371

AN:

877854

Other (OTH)

AF:

0.263

AC:

13181

AN:

50068

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

10441

20882

31322

41763

52204

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7522

15044

22566

30088

37610

<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:

0.283

AC:

43021

AN:

151980

Hom.:

6372

Cov.:

AF XY:

0.278

AC XY:

20670

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.334

AC:

13840

AN:

41380

American (AMR)

AF:

0.239

AC:

3650

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.244

AC:

846

AN:

3472

East Asian (EAS)

AF:

0.117

AC:

607

AN:

5180

South Asian (SAS)

AF:

0.310

AC:

1491

AN:

4810

European-Finnish (FIN)

AF:

0.216

AC:

2290

AN:

10578

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.285

AC:

19340

AN:

67972

Other (OTH)

AF:

0.264

AC:

556

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1541

3082

4622

6163

7704

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

432

864

1296

1728

2160

<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:

0.290

Hom.:

859

Bravo

AF:

0.286

Asia WGS

AF:

0.217

AC:

754

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

7.7

(source)

DANN

Benign

0.67

PhyloP100

-0.26

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