rs12176317

Positions:

• chr6-26372558-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007047.5(BTN3A2):​c.716-339A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0829 in 255,654 control chromosomes in the GnomAD database, including 1,101 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 (555 hom., cov: 32)
  • Exomes 𝑓: 0.093 (546 hom.)
• Consequence: BTN3A2 NM_007047.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTN3A2	NM_007047.5	c.716-339A>G		intron_variant		ENST00000377708.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTN3A2	ENST00000377708.7	c.716-339A>G		intron_variant		1	NM_007047.5	P2
	ENST00000707189.1	n.1000-180629A>G		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-160147A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0764 AC: 11621 AN: 152156 Hom.: 556 Cov.: 32

Gnomad AFR AF: 0.0340

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.0400

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0861

Gnomad SAS AF: 0.0980

Gnomad FIN AF: 0.0709

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0686

GnomAD4 exome AF: 0.0927 AC: 9587 AN: 103380 Hom.: 546 AF XY: 0.0931 AC XY: 5060 AN XY: 54322

Gnomad4 AFR exome AF: 0.0346

Gnomad4 AMR exome AF: 0.0370

Gnomad4 ASJ exome AF: 0.0331

Gnomad4 EAS exome AF: 0.0803

Gnomad4 SAS exome AF: 0.0921

Gnomad4 FIN exome AF: 0.0918

Gnomad4 NFE exome AF: 0.105

Gnomad4 OTH exome AF: 0.0851

GnomAD4 genome AF: 0.0763 AC: 11612 AN: 152274 Hom.: 555 Cov.: 32 AF XY: 0.0732 AC XY: 5453 AN XY: 74466

Gnomad4 AFR AF: 0.0340

Gnomad4 AMR AF: 0.0398

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.0863

Gnomad4 SAS AF: 0.0968

Gnomad4 FIN AF: 0.0709

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0688

Alfa AF: 0.0998 Hom.: 1016

Bravo AF: 0.0712

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.7
DANN	Benign	0.57

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

LitVar

Other links and lift over

dbSNP: rs12176317; hg19: chr6-26372786;