rs2073531

Variant names:

• chr6-26375028-A-G
• rs2073531
• NM_007047.5:c.*34+230A>G

Variant summary

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

The NM_007047.5(BTN3A2):​c.*34+230A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0821 in 419,614 control chromosomes in the GnomAD database, including 1,728 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 (554 hom., cov: 31)
  • Exomes 𝑓: 0.085 (1174 hom.)
• Consequence: BTN3A2 NM_007047.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 14 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=-0.91).
• 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 rank	MANE	Protein	UniProt
BTN3A2	NM_007047.5	c.*34+230A>G		intron_variant	Intron 10 of 10	ENST00000377708.7	NP_008978.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTN3A2	ENST00000377708.7	c.*34+230A>G		intron_variant	Intron 10 of 10	1	NM_007047.5	ENSP00000366937.2

Frequencies

GnomAD3 genomes AF: 0.0764 AC: 11609 AN: 152006 Hom.: 555 Cov.: 31

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.0401

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0862

Gnomad SAS AF: 0.0971

Gnomad FIN AF: 0.0709

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0672

GnomAD4 exome AF: 0.0855 AC: 22857 AN: 267488 Hom.: 1174 Cov.: 4 AF XY: 0.0861 AC XY: 11846 AN XY: 137634

African (AFR) AF: 0.0336 AC: 258 AN: 7680

American (AMR) AF: 0.0363 AC: 347 AN: 9568

Ashkenazi Jewish (ASJ) AF: 0.0299 AC: 270 AN: 9034

East Asian (EAS) AF: 0.0856 AC: 1839 AN: 21496

South Asian (SAS) AF: 0.0757 AC: 924 AN: 12204

European-Finnish (FIN) AF: 0.0669 AC: 1217 AN: 18190

Middle Eastern (MID) AF: 0.0523 AC: 68 AN: 1300

European-Non Finnish (NFE) AF: 0.0972 AC: 16662 AN: 171346

Other (OTH) AF: 0.0763 AC: 1272 AN: 16670

GnomAD4 genome AF: 0.0763 AC: 11600 AN: 152126 Hom.: 554 Cov.: 31 AF XY: 0.0731 AC XY: 5440 AN XY: 74370

African (AFR) AF: 0.0341 AC: 1414 AN: 41524

American (AMR) AF: 0.0399 AC: 610 AN: 15286

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

East Asian (EAS) AF: 0.0864 AC: 446 AN: 5160

South Asian (SAS) AF: 0.0959 AC: 462 AN: 4816

European-Finnish (FIN) AF: 0.0709 AC: 752 AN: 10600

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

European-Non Finnish (NFE) AF: 0.110 AC: 7483 AN: 67958

Other (OTH) AF: 0.0675 AC: 142 AN: 2104

Alfa AF: 0.0939 Hom.: 97

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	-0.91
CADD	Benign	0.37
DANN	Benign	0.78
PhyloP100		-0.40
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: rs2073531; hg19: chr6-26375256;