rs9379859

Variant names:

• chr6-26369321-C-T
• rs9379859
• NM_007047.5:c.433+409C>T

Variant summary

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

The NM_007047.5(BTN3A2):​c.433+409C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0769 in 152,226 control chromosomes in the GnomAD database, including 563 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 (563 hom., cov: 31)
• Consequence: BTN3A2 NM_007047.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 37 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=-0.9).
• 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.433+409C>T		intron_variant	Intron 4 of 10	ENST00000377708.7	NP_008978.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTN3A2	ENST00000377708.7	c.433+409C>T		intron_variant	Intron 4 of 10	1	NM_007047.5	ENSP00000366937.2

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11708 AN: 152108 Hom.: 564 Cov.: 31

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0864

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0698

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

GnomAD4 genome AF: 0.0769 AC: 11699 AN: 152226 Hom.: 563 Cov.: 31 AF XY: 0.0737 AC XY: 5489 AN XY: 74428

African (AFR) AF: 0.0344 AC: 1428 AN: 41546

American (AMR) AF: 0.0408 AC: 624 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3470

East Asian (EAS) AF: 0.0866 AC: 448 AN: 5176

South Asian (SAS) AF: 0.0966 AC: 466 AN: 4822

European-Finnish (FIN) AF: 0.0713 AC: 756 AN: 10598

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

European-Non Finnish (NFE) AF: 0.111 AC: 7538 AN: 68008

Other (OTH) AF: 0.0700 AC: 148 AN: 2114

Alfa AF: 0.0993 Hom.: 2761

Bravo AF: 0.0720

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	-0.90
CADD	Benign	2.5
DANN	Benign	0.59
PhyloP100		0.19
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: rs9379859; hg19: chr6-26369549;