rs9104

Variant names:

• chr6-26377921-G-A
• rs9104
• NM_007047.5:c.*2159G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 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=-0.88).
• 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 rank	MANE	Protein	UniProt
BTN3A2	NM_007047.5	c.*2159G>A		3_prime_UTR_variant	Exon 11 of 11	ENST00000377708.7	NP_008978.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTN3A2	ENST00000377708.7	c.*2159G>A		3_prime_UTR_variant	Exon 11 of 11	1	NM_007047.5	ENSP00000366937.2

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.0938 AC: 3 AN: 32

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.125 AC: 1 AN: 8

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.115 AC: 31 AN: 270

Other (OTH) AF: 0.125 AC: 2 AN: 16

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

African (AFR) AF: 0.218 AC: 9027 AN: 41466

American (AMR) AF: 0.151 AC: 2309 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 623 AN: 3472

East Asian (EAS) AF: 0.0439 AC: 227 AN: 5176

South Asian (SAS) AF: 0.177 AC: 851 AN: 4818

European-Finnish (FIN) AF: 0.135 AC: 1432 AN: 10582

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9149 AN: 67998

Other (OTH) AF: 0.142 AC: 300 AN: 2112

Alfa AF: 0.134 Hom.: 1303

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
PhyloP100		-0.016
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: rs9104; hg19: chr6-26378149;