Genetic Variant ENST00000466808.2:n.1067+105G>A (chr6-26426628-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 ENST00000466808.2(BTN2A3P):n.1067+105G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0912 in 711,296 control chromosomes in the GnomAD database, including 3,620 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 0.077 ( 558 hom., cov: 31)

Exomes 𝑓: 0.095 ( 3062 hom. )

Consequence

BTN2A3P
ENST00000466808.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.226

Publications

17 publications found

Variant links:

Genes affected

BTN2A3P (HGNC:):

BTN2A3P links:

BTN2A3P (HGNC:13229): (butyrophilin subfamily 2 member A3, pseudogene) The butyrophilin (BTN) genes are a group of major histocompatibility complex (MHC)-associated genes that encode type I membrane proteins with 2 extracellular immunoglobulin (Ig) domains and an intracellular B30.2 (PRYSPRY) domain. Three subfamilies of human BTN genes are located in the MHC class I region: the single-copy BTN1A1 gene (MIM 601610) and the BTN2 (e.g., BTN2A3) and BTN3 (e.g., BNT3A1; MIM 613593) genes, which have undergone tandem duplication, resulting in 3 copies of each (summary by Smith et al., 2010 [PubMed 20208008]).[supplied by OMIM, Nov 2010]

BTN2A3P 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTN2A3P	NR_027795.1 link	n.1452+105G>A		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
BTN2A3P	ENST00000466808.2 link	n.1067+105G>A	intron_variant	Intron 4 of 6	1
BTN2A3P	ENST00000377662.6 link	n.706+105G>A	intron_variant	Intron 3 of 5	6
BTN2A3P	ENST00000463944.2 link	n.1433+105G>A	intron_variant	Intron 5 of 5	4

Frequencies

GnomAD3 genomes

AF:

0.0768

AC:

11674

AN:

152074

Hom.:

559

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0335

Gnomad AMI

AF:

0.196

Gnomad AMR

AF:

0.0379

Gnomad ASJ

AF:

0.0375

Gnomad EAS

AF:

0.100

Gnomad SAS

AF:

0.0993

Gnomad FIN

AF:

0.0771

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.109

Gnomad OTH

AF:

0.0632

GnomAD4 exome

AF:

0.0952

AC:

53236

AN:

559104

Hom.:

3062

AF XY:

0.0959

AC XY:

28507

AN XY:

297220

show subpopulations

African (AFR)

AF:

0.0354

AC:

525

AN:

14826

American (AMR)

AF:

0.0321

AC:

1026

AN:

31948

Ashkenazi Jewish (ASJ)

AF:

0.0412

AC:

548

AN:

13304

East Asian (EAS)

AF:

0.123

AC:

3224

AN:

26198

South Asian (SAS)

AF:

0.0921

AC:

5362

AN:

58222

European-Finnish (FIN)

AF:

0.0832

AC:

3217

AN:

38652

Middle Eastern (MID)

AF:

0.0416

AC:

143

AN:

3440

European-Non Finnish (NFE)

AF:

0.107

AC:

36850

AN:

345610

Other (OTH)

AF:

0.0870

AC:

2341

AN:

26904

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

2158

4316

6474

8632

10790

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

642

1284

1926

2568

3210

<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:

0.0767

AC:

11667

AN:

152192

Hom.:

558

Cov.:

AF XY:

0.0740

AC XY:

5509

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.0334

AC:

1388

AN:

41518

American (AMR)

AF:

0.0377

AC:

577

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0375

AC:

130

AN:

3468

East Asian (EAS)

AF:

0.100

AC:

520

AN:

5182

South Asian (SAS)

AF:

0.0983

AC:

475

AN:

4830

European-Finnish (FIN)

AF:

0.0771

AC:

817

AN:

10600

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.109

AC:

7439

AN:

67986

Other (OTH)

AF:

0.0635

AC:

134

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

537

1075

1612

2150

2687

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:

0.0907

Hom.:

905

Bravo

AF:

0.0711

Asia WGS

AF:

0.105

AC:

363

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.0

(source)

DANN

Benign

0.60

PhyloP100

0.23

Splicing

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