6-26377713-C-G

Variant names:

• chr6-26377713-C-G
• rs14232
• NM_007047.5:c.*1951C>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.*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
• Publications: 7 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007047.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTN3A2	NM_007047.5	MANE Select	c.*1951C>G		3_prime_UTR	Exon 11 of 11	NP_008978.2
	BTN3A2	NM_001197246.2		c.*1219C>G		3_prime_UTR	Exon 9 of 9	NP_001184175.1	P78410-1
	BTN3A2	NM_001197247.3		c.*2233C>G		3_prime_UTR	Exon 11 of 11	NP_001184176.1	P78410-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTN3A2	ENST00000377708.7	TSL:1 MANE Select	c.*1951C>G		3_prime_UTR	Exon 11 of 11	ENSP00000366937.2	P78410-1
	BTN3A2	ENST00000872162.1		c.*1951C>G		3_prime_UTR	Exon 11 of 11	ENSP00000542221.1
	BTN3A2	ENST00000957869.1		c.*1175C>G		3_prime_UTR	Exon 11 of 11	ENSP00000627928.1

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

African (AFR) AF: 0.200 AC: 97 AN: 486

American (AMR) AF: 0.168 AC: 554 AN: 3304

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 81 AN: 450

East Asian (EAS) AF: 0.0286 AC: 42 AN: 1466

South Asian (SAS) AF: 0.196 AC: 733 AN: 3736

European-Finnish (FIN) AF: 0.154 AC: 95 AN: 616

Middle Eastern (MID) AF: 0.265 AC: 18 AN: 68

European-Non Finnish (NFE) AF: 0.139 AC: 2097 AN: 15062

Other (OTH) AF: 0.140 AC: 167 AN: 1190

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

African (AFR) AF: 0.216 AC: 8957 AN: 41422

American (AMR) AF: 0.171 AC: 2608 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3470

East Asian (EAS) AF: 0.0319 AC: 165 AN: 5174

South Asian (SAS) AF: 0.177 AC: 853 AN: 4818

European-Finnish (FIN) AF: 0.136 AC: 1434 AN: 10580

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9545 AN: 68006

Other (OTH) AF: 0.149 AC: 314 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.36
PhyloP100		-0.80
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs14232; hg19: chr6-26377941;