6-132619154-C-T

Variant names:

• chr6-132619154-C-T
• rs4451148
• NM_001033080.1:c.61-1009G>A

Variant summary

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

The NM_001033080.1(TAAR2):​c.61-1009G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,074 control chromosomes in the GnomAD database, including 5,514 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 0.24 (5514 hom., cov: 32)
• Consequence: TAAR2 NM_001033080.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR2	NM_001033080.1	c.61-1009G>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.61-1009G>A		intron_variant	Intron 1 of 1	1	NM_001033080.1	ENSP00000356908.1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37191 AN: 151956 Hom.: 5518 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.245 AC: 37183 AN: 152074 Hom.: 5514 Cov.: 32 AF XY: 0.252 AC XY: 18693 AN XY: 74312

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.236

Alfa AF: 0.264 Hom.: 5857

Bravo AF: 0.233

Asia WGS AF: 0.442 AC: 1534 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4451148; hg19: chr6-132940293;