chr6-26377713-C-G

Position:

• chr6-26377713-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007047.5(BTN3A2):​c.*1951C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 178,440 control chromosomes in the GnomAD database, including 2,526 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 0.16 (2191 hom., cov: 32)
  • Exomes 𝑓: 0.15 (335 hom.)
• Consequence: BTN3A2 NM_007047.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.802

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTN3A2	NM_007047.5	c.*1951C>G		3_prime_UTR_variant	11/11	ENST00000377708.7	NP_008978.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTN3A2	ENST00000377708.7	c.*1951C>G		3_prime_UTR_variant	11/11	1	NM_007047.5	ENSP00000366937	P2
	ENST00000707189.1	n.1000-175474C>G		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-154992C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24713 AN: 151944 Hom.: 2191 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0314

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.150

GnomAD4 exome AF: 0.147 AC: 3884 AN: 26378 Hom.: 335 Cov.: 0 AF XY: 0.149 AC XY: 2093 AN XY: 14056

Gnomad4 AFR exome AF: 0.200

Gnomad4 AMR exome AF: 0.168

Gnomad4 ASJ exome AF: 0.180

Gnomad4 EAS exome AF: 0.0286

Gnomad4 SAS exome AF: 0.196

Gnomad4 FIN exome AF: 0.154

Gnomad4 NFE exome AF: 0.139

Gnomad4 OTH exome AF: 0.140

GnomAD4 genome AF: 0.163 AC: 24738 AN: 152062 Hom.: 2191 Cov.: 32 AF XY: 0.162 AC XY: 12045 AN XY: 74308

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.0319

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.149

Alfa AF: 0.0778 Hom.: 100

Bravo AF: 0.168

Asia WGS AF: 0.0880 AC: 306 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	0.95
DANN	Benign	0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs14232; hg19: chr6-26377941;