rs12199613

Variant names:

• chr6-26366990-C-T
• rs12199613
• NM_007047.5:c.-66-1000C>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.-66-1000C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152,062 control chromosomes in the GnomAD database, including 11,122 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 0.38 (11122 hom., cov: 32)
• Consequence: BTN3A2 NM_007047.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.710
• Publications: 18 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTN3A2	NM_007047.5	c.-66-1000C>T		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.-66-1000C>T		intron_variant	Intron 1 of 10	1	NM_007047.5	ENSP00000366937.2

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57277 AN: 151944 Hom.: 11114 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.377 AC: 57303 AN: 152062 Hom.: 11122 Cov.: 32 AF XY: 0.375 AC XY: 27841 AN XY: 74336

African (AFR) AF: 0.421 AC: 17474 AN: 41460

American (AMR) AF: 0.329 AC: 5032 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1010 AN: 3468

East Asian (EAS) AF: 0.219 AC: 1137 AN: 5182

South Asian (SAS) AF: 0.331 AC: 1596 AN: 4818

European-Finnish (FIN) AF: 0.401 AC: 4231 AN: 10550

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25558 AN: 67982

Other (OTH) AF: 0.339 AC: 716 AN: 2114

Alfa AF: 0.375 Hom.: 21944

Bravo AF: 0.375

Asia WGS AF: 0.260 AC: 905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.48
PhyloP100		-0.71
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: rs12199613; hg19: chr6-26367218;