dbSNP rs9104: BTN3A2:c.*2159G>A (chr6-26377921-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007047.5(BTN3A2):c.*2159G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,460 control chromosomes in the GnomAD database, including 2,042 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 0.16 ( 2036 hom., cov: 32)

Exomes 𝑓: 0.11 ( 6 hom. )

Consequence

BTN3A2
NM_007047.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0160

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTN3A2	NM_007047.5 link	c.*2159G>A		3_prime_UTR_variant	Exon 11 of 11	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.*2159G>A		3_prime_UTR_variant	Exon 11 of 11	1	NM_007047.5	ENSP00000366937.2		P78410-1

Frequencies

GnomAD3 genomes

AF:

0.159

AC:

24096

AN:

152012

Hom.:

2037

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.179

Gnomad EAS

AF:

0.0434

Gnomad SAS

AF:

0.176

Gnomad FIN

AF:

0.135

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.144

GnomAD4 exome

AF:

0.114

AC:

AN:

332

Hom.:

Cov.:

AF XY:

0.118

AC XY:

AN XY:

170

show subpopulations

Gnomad4 AMR exome

AF:

0.0938

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.125

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.115

Gnomad4 OTH exome

AF:

0.125

GnomAD4 genome

AF:

0.159

AC:

24115

AN:

152128

Hom.:

2036

Cov.:

AF XY:

0.157

AC XY:

11690

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.218

Gnomad4 AMR

AF:

0.151

Gnomad4 ASJ

AF:

0.179

Gnomad4 EAS

AF:

0.0439

Gnomad4 SAS

AF:

0.177

Gnomad4 FIN

AF:

0.135

Gnomad4 NFE

AF:

0.135

Gnomad4 OTH

AF:

0.142

Alfa

AF:

0.121

Hom.:

487

Bravo

AF:

0.162

Asia WGS

AF:

0.0930

AC:

324

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.6

DANN

Benign

0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over