Genetic Variant ENSG00000291336:n.1000-99673A>G (chr6-26453514-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 ENST00000707189.1(ENSG00000291336):n.1000-99673A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 151,920 control chromosomes in the GnomAD database, including 1,252 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 0.12 ( 1251 hom., cov: 31)

Exomes 𝑓: 0.17 ( 1 hom. )

Consequence

ENSG00000291336
ENST00000707189.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.53

Publications

10 publications found

Variant links:

Genes affected

ENSG00000291336 (HGNC:):

ENSG00000291336 links:

BTN3A3 (HGNC:1140): (butyrophilin subfamily 3 member A3) 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., BTN2A1; MIM 613590) and BTN3 (e.g., BNT3A3) 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]

BTN3A3 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 = 0.122 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000707189.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BTN3A3	NM_006994.5	MANE Select	c.*1103A>G	downstream_gene	N/A	NP_008925.1
BTN3A3	NM_197974.3		c.*1103A>G	downstream_gene	N/A	NP_932078.2
BTN3A3	NM_001242803.2		c.*1103A>G	downstream_gene	N/A	NP_001229732.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ENSG00000291336	ENST00000707189.1		n.1000-99673A>G	intron	N/A
ENSG00000291338	ENST00000707191.1		n.1001-79191A>G	intron	N/A
BTN3A3	ENST00000244519.7	TSL:1 MANE Select	c.*1103A>G	downstream_gene	N/A	ENSP00000244519.2

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

18938

AN:

151780

Hom.:

1251

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.139

Gnomad AMR

AF:

0.112

Gnomad ASJ

AF:

0.0904

Gnomad EAS

AF:

0.0779

Gnomad SAS

AF:

0.0437

Gnomad FIN

AF:

0.222

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.119

GnomAD4 exome

AF:

0.167

AC:

AN:

Hom.:

AF XY:

0.167

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.167

AC:

AN:

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.125

AC:

18945

AN:

151896

Hom.:

1251

Cov.:

AF XY:

0.127

AC XY:

9426

AN XY:

74214

show subpopulations

African (AFR)

AF:

0.124

AC:

5124

AN:

41394

American (AMR)

AF:

0.111

AC:

1703

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0904

AC:

314

AN:

3472

East Asian (EAS)

AF:

0.0773

AC:

400

AN:

5172

South Asian (SAS)

AF:

0.0433

AC:

209

AN:

4822

European-Finnish (FIN)

AF:

0.222

AC:

2329

AN:

10494

Middle Eastern (MID)

AF:

0.0788

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.125

AC:

8469

AN:

67952

Other (OTH)

AF:

0.117

AC:

247

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

863

1726

2588

3451

4314

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

202

404

606

808

1010

<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:

0.120

Hom.:

1976

Bravo

AF:

0.119

Asia WGS

AF:

0.0460

AC:

163

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.7

(source)

DANN

Benign

0.73

PhyloP100

1.5

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over