rs9389015

Variant names:

• chr6-132622297-C-T
• rs9389015
• NM_001033080.1:c.60+1919G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001033080.1(TAAR2):​c.60+1919G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 150,844 control chromosomes in the GnomAD database, including 31,029 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 0.63 (31029 hom., cov: 29)
• Consequence: TAAR2 NM_001033080.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• Publications: 6 publications found

Genes affected

TAAR2 (HGNC:4514): (trace amine associated receptor 2) Predicted to enable trace-amine receptor activity. Predicted to be involved in G protein-coupled receptor signaling pathway. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000290584 (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 (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR2	NM_001033080.1	c.60+1919G>A		intron_variant	Intron 1 of 1	ENST00000367931.1	NP_001028252.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAAR2	ENST00000367931.1	c.60+1919G>A		intron_variant	Intron 1 of 1	1	NM_001033080.1	ENSP00000356908.1
ENSG00000290584	ENST00000466706.2	n.171-5552G>A		intron_variant	Intron 1 of 2	6

Frequencies

GnomAD3 genomes AF: 0.627 AC: 94542 AN: 150726 Hom.: 30984 Cov.: 29

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.620

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.627 AC: 94643 AN: 150844 Hom.: 31029 Cov.: 29 AF XY: 0.629 AC XY: 46356 AN XY: 73674

African (AFR) AF: 0.811 AC: 33498 AN: 41324

American (AMR) AF: 0.563 AC: 8520 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2006 AN: 3464

East Asian (EAS) AF: 0.842 AC: 4335 AN: 5146

South Asian (SAS) AF: 0.654 AC: 3126 AN: 4782

European-Finnish (FIN) AF: 0.532 AC: 5330 AN: 10016

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.531 AC: 35930 AN: 67690

Other (OTH) AF: 0.620 AC: 1297 AN: 2092

Alfa AF: 0.561 Hom.: 46360

Bravo AF: 0.634

Asia WGS AF: 0.761 AC: 2622 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.72
DANN	Benign	0.19
PhyloP100		-0.28
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: rs9389015; hg19: chr6-132943436;