dbSNP rs2072806: BTN2A2:c.95-150C>G (chr6-26384865-C-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_006995.5(BTN2A2):c.95-150C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 853,386 control chromosomes in the GnomAD database, including 5,252 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 0.079 ( 592 hom., cov: 32)

Exomes 𝑓: 0.11 ( 4660 hom. )

Consequence

BTN2A2
NM_006995.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.157

Publications

24 publications found

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:

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=-0.77).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTN2A2	NM_006995.5 link	c.95-150C>G		intron_variant	Intron 2 of 7	ENST00000356709.9	NP_008926.2	Q8WVV5-1A0A024R038

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTN2A2	ENST00000356709.9 link	c.95-150C>G		intron_variant	Intron 2 of 7	1	NM_006995.5	ENSP00000349143.4		Q8WVV5-1

Frequencies

GnomAD3 genomes

AF:

0.0788

AC:

11984

AN:

152166

Hom.:

594

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0339

Gnomad AMI

AF:

0.198

Gnomad AMR

AF:

0.0393

Gnomad ASJ

AF:

0.0415

Gnomad EAS

AF:

0.102

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.0789

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.0661

GnomAD4 exome

AF:

0.107

AC:

75157

AN:

701102

Hom.:

4660

AF XY:

0.106

AC XY:

37900

AN XY:

356050

show subpopulations

African (AFR)

AF:

0.0343

AC:

577

AN:

16822

American (AMR)

AF:

0.0362

AC:

687

AN:

18972

Ashkenazi Jewish (ASJ)

AF:

0.0452

AC:

690

AN:

15260

East Asian (EAS)

AF:

0.134

AC:

4325

AN:

32200

South Asian (SAS)

AF:

0.0917

AC:

4470

AN:

48754

European-Finnish (FIN)

AF:

0.0831

AC:

2869

AN:

34506

Middle Eastern (MID)

AF:

0.0473

AC:

183

AN:

3870

European-Non Finnish (NFE)

AF:

0.117

AC:

58182

AN:

496428

Other (OTH)

AF:

0.0926

AC:

3174

AN:

34290

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

3192

6385

9577

12770

15962

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1526

3052

4578

6104

7630

<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:

0.0786

AC:

11975

AN:

152284

Hom.:

592

Cov.:

AF XY:

0.0759

AC XY:

5652

AN XY:

74460

show subpopulations

African (AFR)

AF:

0.0339

AC:

1408

AN:

41552

American (AMR)

AF:

0.0391

AC:

599

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.0415

AC:

144

AN:

3470

East Asian (EAS)

AF:

0.103

AC:

533

AN:

5188

South Asian (SAS)

AF:

0.101

AC:

488

AN:

4826

European-Finnish (FIN)

AF:

0.0789

AC:

837

AN:

10610

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.112

AC:

7633

AN:

68014

Other (OTH)

AF:

0.0664

AC:

140

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

561

1122

1682

2243

2804

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

142

284

426

568

710

<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:

0.0988

Hom.:

Bravo

AF:

0.0732

Asia WGS

AF:

0.103

AC:

359

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

8.0

(source)

DANN

Benign

0.73

PhyloP100

0.16

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