rs9104

Positions:

• chr6-26377921-G-A
• chr6-26377921-G-C
• chr6-26377921-G-T

Variant summary

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

The NM_007047.5(BTN3A2):​c.*2159G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,460 control chromosomes in the GnomAD database, including 2,042 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 (2036 hom., cov: 32)
  • Exomes 𝑓: 0.11 (6 hom.)
• Consequence: BTN3A2 NM_007047.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTN3A2	NM_007047.5	c.*2159G>A		3_prime_UTR_variant	11/11	ENST00000377708.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTN3A2	ENST00000377708.7	c.*2159G>A		3_prime_UTR_variant	11/11	1	NM_007047.5	P2
	ENST00000707189.1	n.1000-175266G>A		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-154784G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24096 AN: 152012 Hom.: 2037 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.0434

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.144

GnomAD4 exome AF: 0.114 AC: 38 AN: 332 Hom.: 6 Cov.: 0 AF XY: 0.118 AC XY: 20 AN XY: 170

Gnomad4 AMR exome AF: 0.0938

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.125

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.115

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.159 AC: 24115 AN: 152128 Hom.: 2036 Cov.: 32 AF XY: 0.157 AC XY: 11690 AN XY: 74368

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.0439

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.142

Alfa AF: 0.121 Hom.: 487

Bravo AF: 0.162

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9104; hg19: chr6-26378149;