rs733528

Variant names:

• chr6-26374675-A-G
• rs733528
• NM_007047.5:c.*7-96A>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.*7-96A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 1,326,676 control chromosomes in the GnomAD database, including 50,699 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 0.28 (6372 hom., cov: 30)
  • Exomes 𝑓: 0.27 (44327 hom.)
• Consequence: BTN3A2 NM_007047.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 10 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTN3A2	NM_007047.5	c.*7-96A>G		intron_variant	Intron 9 of 10	ENST00000377708.7	NP_008978.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTN3A2	ENST00000377708.7	c.*7-96A>G		intron_variant	Intron 9 of 10	1	NM_007047.5	ENSP00000366937.2

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42990 AN: 151862 Hom.: 6364 Cov.: 30

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.265

GnomAD4 exome AF: 0.271 AC: 318162 AN: 1174696 Hom.: 44327 Cov.: 18 AF XY: 0.272 AC XY: 161136 AN XY: 592378

African (AFR) AF: 0.336 AC: 9019 AN: 26850

American (AMR) AF: 0.246 AC: 8711 AN: 35396

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 5186 AN: 20786

East Asian (EAS) AF: 0.105 AC: 4024 AN: 38256

South Asian (SAS) AF: 0.301 AC: 21555 AN: 71506

European-Finnish (FIN) AF: 0.223 AC: 11239 AN: 50316

Middle Eastern (MID) AF: 0.239 AC: 876 AN: 3664

European-Non Finnish (NFE) AF: 0.278 AC: 244371 AN: 877854

Other (OTH) AF: 0.263 AC: 13181 AN: 50068

GnomAD4 genome AF: 0.283 AC: 43021 AN: 151980 Hom.: 6372 Cov.: 30 AF XY: 0.278 AC XY: 20670 AN XY: 74284

African (AFR) AF: 0.334 AC: 13840 AN: 41380

American (AMR) AF: 0.239 AC: 3650 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 846 AN: 3472

East Asian (EAS) AF: 0.117 AC: 607 AN: 5180

South Asian (SAS) AF: 0.310 AC: 1491 AN: 4810

European-Finnish (FIN) AF: 0.216 AC: 2290 AN: 10578

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19340 AN: 67972

Other (OTH) AF: 0.264 AC: 556 AN: 2110

Alfa AF: 0.290 Hom.: 859

Bravo AF: 0.286

Asia WGS AF: 0.217 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.7
DANN	Benign	0.67
PhyloP100		-0.26
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: rs733528; hg19: chr6-26374903; COSMIC: COSV62687310; COSMIC: COSV62687310;