rs9379858

Variant names:

• chr6-26367461-T-C
• rs9379858
• NM_007047.5:c.-66-529T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007047.5(BTN3A2):​c.-66-529T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0768 in 152,258 control chromosomes in the GnomAD database, including 564 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 (564 hom., cov: 32)
• Consequence: BTN3A2 NM_007047.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 29 publications found

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]

ENSG00000291336 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTN3A2	NM_007047.5	c.-66-529T>C		intron_variant	Intron 1 of 10	ENST00000377708.7	NP_008978.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTN3A2	ENST00000377708.7	c.-66-529T>C		intron_variant	Intron 1 of 10	1	NM_007047.5	ENSP00000366937.2

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11708 AN: 152142 Hom.: 565 Cov.: 32

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.0409

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0861

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0686

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0768 AC: 11699 AN: 152258 Hom.: 564 Cov.: 32 AF XY: 0.0738 AC XY: 5492 AN XY: 74460

African (AFR) AF: 0.0344 AC: 1429 AN: 41562

American (AMR) AF: 0.0407 AC: 623 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3472

East Asian (EAS) AF: 0.0863 AC: 447 AN: 5182

South Asian (SAS) AF: 0.0969 AC: 468 AN: 4830

European-Finnish (FIN) AF: 0.0713 AC: 756 AN: 10604

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7540 AN: 68000

Other (OTH) AF: 0.0688 AC: 145 AN: 2108

Alfa AF: 0.103 Hom.: 2122

Bravo AF: 0.0720

Asia WGS AF: 0.0980 AC: 342 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	0.14
DANN	Benign	0.36
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9379858; hg19: chr6-26367689;