6-132623858-G-A

Variant names:

• chr6-132623858-G-A
• rs4129256
• NM_001033080.1:c.60+358C>T

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+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
• 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=-0.82).
• 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 rank	MANE	Protein	UniProt
TAAR2	NM_001033080.1	c.60+358C>T		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+358C>T		intron_variant	Intron 1 of 1	1	NM_001033080.1	ENSP00000356908.1
ENSG00000290584	ENST00000466706.2	n.171-7113C>T		intron_variant	Intron 1 of 2	6

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

African (AFR) AF: 0.105 AC: 4343 AN: 41426

American (AMR) AF: 0.212 AC: 3226 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 724 AN: 3470

East Asian (EAS) AF: 0.142 AC: 731 AN: 5132

South Asian (SAS) AF: 0.224 AC: 1079 AN: 4808

European-Finnish (FIN) AF: 0.183 AC: 1927 AN: 10516

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13917 AN: 67942

Other (OTH) AF: 0.183 AC: 386 AN: 2110

Alfa AF: 0.195 Hom.: 9609

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
PhyloP100		-0.81
PromoterAI		0.0079	Neutral
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: rs4129256; hg19: chr6-132944997;