Genetic Variant BTN3A2:c.*34+230A>G (chr6-26375028-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.*34+230A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0821 in 419,614 control chromosomes in the GnomAD database, including 1,728 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 ( 554 hom., cov: 31)

Exomes 𝑓: 0.085 ( 1174 hom. )

Consequence

BTN3A2
NM_007047.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.395

Publications

14 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=-0.91).

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007047.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BTN3A2	NM_007047.5	MANE Select	c.*34+230A>G	intron	N/A	NP_008978.2
BTN3A2	NM_001197246.2		c.*34+230A>G	intron	N/A	NP_001184175.1
BTN3A2	NM_001197247.3		c.*34+230A>G	intron	N/A	NP_001184176.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BTN3A2	ENST00000377708.7	TSL:1 MANE Select	c.*34+230A>G	intron	N/A	ENSP00000366937.2
BTN3A2	ENST00000604202.1	TSL:6	n.2336A>G	non_coding_transcript_exon	Exon 1 of 1
BTN3A2	ENST00000356386.6	TSL:5	c.*34+230A>G	intron	N/A	ENSP00000348751.2

Frequencies

GnomAD3 genomes

AF:

0.0764

AC:

11609

AN:

152006

Hom.:

555

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0341

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.0401

Gnomad ASJ

AF:

0.0297

Gnomad EAS

AF:

0.0862

Gnomad SAS

AF:

0.0971

Gnomad FIN

AF:

0.0709

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.110

Gnomad OTH

AF:

0.0672

GnomAD4 exome

AF:

0.0855

AC:

22857

AN:

267488

Hom.:

1174

Cov.:

AF XY:

0.0861

AC XY:

11846

AN XY:

137634

show subpopulations

African (AFR)

AF:

0.0336

AC:

258

AN:

7680

American (AMR)

AF:

0.0363

AC:

347

AN:

9568

Ashkenazi Jewish (ASJ)

AF:

0.0299

AC:

270

AN:

9034

East Asian (EAS)

AF:

0.0856

AC:

1839

AN:

21496

South Asian (SAS)

AF:

0.0757

AC:

924

AN:

12204

European-Finnish (FIN)

AF:

0.0669

AC:

1217

AN:

18190

Middle Eastern (MID)

AF:

0.0523

AC:

AN:

1300

European-Non Finnish (NFE)

AF:

0.0972

AC:

16662

AN:

171346

Other (OTH)

AF:

0.0763

AC:

1272

AN:

16670

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

936

1872

2808

3744

4680

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

110

220

330

440

550

<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:

11600

AN:

152126

Hom.:

554

Cov.:

AF XY:

0.0731

AC XY:

5440

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.0341

AC:

1414

AN:

41524

American (AMR)

AF:

0.0399

AC:

610

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0297

AC:

103

AN:

3472

East Asian (EAS)

AF:

0.0864

AC:

446

AN:

5160

South Asian (SAS)

AF:

0.0959

AC:

462

AN:

4816

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:

7483

AN:

67958

Other (OTH)

AF:

0.0675

AC:

142

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

550

1100

1649

2199

2749

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:

0.0939

Hom.:

Bravo

AF:

0.0712

Asia WGS

AF:

0.0990

AC:

343

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.37

(source)

DANN

Benign

0.78

PhyloP100

-0.40

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over