chr6-26374675-A-G

Position:

• chr6-26374675-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
BTN3A2	NM_007047.5	c.*7-96A>G		intron_variant		ENST00000377708.7	NP_008978.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTN3A2	ENST00000377708.7	c.*7-96A>G		intron_variant		1	NM_007047.5	ENSP00000366937	P2
	ENST00000707189.1	n.1000-178512A>G		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-158030A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 0.336

Gnomad4 AMR exome AF: 0.246

Gnomad4 ASJ exome AF: 0.249

Gnomad4 EAS exome AF: 0.105

Gnomad4 SAS exome AF: 0.301

Gnomad4 FIN exome AF: 0.223

Gnomad4 NFE exome AF: 0.278

Gnomad4 OTH exome AF: 0.263

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

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.264

Alfa AF: 0.289 Hom.: 807

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs733528; hg19: chr6-26374903; COSMIC: COSV62687310; COSMIC: COSV62687310;