chr6-132623858-G-A

Position:

• chr6-132623858-G-A

Variant summary

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

The NM_001033080.1(TAAR2):​c.60+358C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,828 control chromosomes in the GnomAD database, including 2,503 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 0.17 (2503 hom., cov: 31)
• Consequence: TAAR2 NM_001033080.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAAR2	NM_001033080.1	c.60+358C>T		intron_variant		ENST00000367931.1	NP_001028252.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAAR2	ENST00000367931.1	c.60+358C>T		intron_variant		1	NM_001033080.1	ENSP00000356908.1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26484 AN: 151708 Hom.: 2500 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.175 AC: 26505 AN: 151828 Hom.: 2503 Cov.: 31 AF XY: 0.175 AC XY: 12963 AN XY: 74170

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.183

Alfa AF: 0.201 Hom.: 6501

Bravo AF: 0.171

Asia WGS AF: 0.170 AC: 590 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.80
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4129256; hg19: chr6-132944997;