rs2745428

chr6-132657859-C-Achr6-132657859-C-Gchr6-132657859-C-T

Variant summary

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

The NM_138327.4(TAAR1):c.-127+1271G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,014 control chromosomes in the GnomAD database, including 51,591 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 0.82 (51591 hom., cov: 33)
• Consequence: TAAR1 NM_138327.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950

Genes affected

TAAR1 (HGNC:17734): (trace amine associated receptor 1) The protein encoded by this gene is a G-protein coupled receptor activated by trace amines. The encoded protein responds little or not at all to dopamine, serotonin, epinephrine, or histamine, but responds well to beta-phenylethylamine, p-tyramine, octopamine, and tryptamine. While primarily functioning in neurologic systems, there is evidence that this gene is involved in blood cell and immunologic functions as well. This gene is thought to be intronless. [provided by RefSeq, Nov 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAAR1	NM_138327.4	c.-127+1271G>T		intron_variant		ENST00000275216.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAAR1	ENST00000275216.3	c.-127+1271G>T		intron_variant			NM_138327.4	P1

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124897 AN: 151896 Hom.: 51558 Cov.: 33

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.822 AC: 124986 AN: 152014 Hom.: 51591 Cov.: 33 AF XY: 0.822 AC XY: 61092 AN XY: 74304

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.814

Alfa AF: 0.800 Hom.: 21256

Bravo AF: 0.826

Asia WGS AF: 0.833 AC: 2869 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.73
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2745428; hg19: chr6-132978998; COSMIC: COSV68647428;