rs14232

Variant names:

• chr6-26377713-C-A
• rs14232
• NM_007047.5:c.*1951C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-26377713-C-A
• chr6-26377713-C-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_007047.5(BTN3A2):​c.*1951C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

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>A		3_prime_UTR	Exon 11 of 11	NP_008978.2
	BTN3A2	NM_001197246.2		c.*1219C>A		3_prime_UTR	Exon 9 of 9	NP_001184175.1	P78410-1
	BTN3A2	NM_001197247.3		c.*2233C>A		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>A		3_prime_UTR	Exon 11 of 11	ENSP00000366937.2	P78410-1
	BTN3A2	ENST00000872162.1		c.*1951C>A		3_prime_UTR	Exon 11 of 11	ENSP00000542221.1
	BTN3A2	ENST00000957869.1		c.*1175C>A		3_prime_UTR	Exon 11 of 11	ENSP00000627928.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 26424 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 14082

African (AFR) AF: 0.00 AC: 0 AN: 488

American (AMR) AF: 0.00 AC: 0 AN: 3310

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 452

East Asian (EAS) AF: 0.00 AC: 0 AN: 1466

South Asian (SAS) AF: 0.00 AC: 0 AN: 3752

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 70

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 15080

Other (OTH) AF: 0.00 AC: 0 AN: 1190

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 100

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.89
DANN	Benign	0.45
PhyloP100		-0.80

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;