rs3813354

Positions:

• chr6-132589495-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_003967.3(TAAR5):​c.192G>A​(p.Ala64=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 1,613,708 control chromosomes in the GnomAD database, including 15,948 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 0.14 (1941 hom., cov: 28)
  • Exomes 𝑓: 0.12 (14007 hom.)
• Consequence: TAAR5 NM_003967.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01

Genes affected

TAAR5 (HGNC:30236): (trace amine associated receptor 5) Enables trimethylamine receptor activity. Predicted to be involved in signal transduction. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BP7: Synonymous conserved (PhyloP=-3.01 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAAR5	NM_003967.3	c.192G>A	p.Ala64=	synonymous_variant	1/1	ENST00000258034.4	NP_003958.2
TAAR5	NM_001389527.1	c.192G>A	p.Ala64=	synonymous_variant	4/4		NP_001376456.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAAR5	ENST00000258034.4	c.192G>A	p.Ala64=	synonymous_variant	1/1		NM_003967.3	ENSP00000258034	P1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21606 AN: 151888 Hom.: 1940 Cov.: 28

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.0704

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.0917

Gnomad OTH AF: 0.170

GnomAD3 exomes AF: 0.161 AC: 40391 AN: 250610 Hom.: 4429 AF XY: 0.165 AC XY: 22299 AN XY: 135402

Gnomad AFR exome AF: 0.177

Gnomad AMR exome AF: 0.214

Gnomad ASJ exome AF: 0.159

Gnomad EAS exome AF: 0.309

Gnomad SAS exome AF: 0.319

Gnomad FIN exome AF: 0.0693

Gnomad NFE exome AF: 0.0941

Gnomad OTH exome AF: 0.156

GnomAD4 exome AF: 0.117 AC: 171393 AN: 1461702 Hom.: 14007 Cov.: 37 AF XY: 0.123 AC XY: 89225 AN XY: 727146

Gnomad4 AFR exome AF: 0.182

Gnomad4 AMR exome AF: 0.212

Gnomad4 ASJ exome AF: 0.156

Gnomad4 EAS exome AF: 0.321

Gnomad4 SAS exome AF: 0.315

Gnomad4 FIN exome AF: 0.0682

Gnomad4 NFE exome AF: 0.0886

Gnomad4 OTH exome AF: 0.142

GnomAD4 genome AF: 0.142 AC: 21625 AN: 152006 Hom.: 1941 Cov.: 28 AF XY: 0.149 AC XY: 11071 AN XY: 74294

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.0704

Gnomad4 NFE AF: 0.0916

Gnomad4 OTH AF: 0.172

Alfa AF: 0.113 Hom.: 1879

Bravo AF: 0.149

Asia WGS AF: 0.323 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	1.2
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3813354; hg19: chr6-132910634; COSMIC: COSV57798573; COSMIC: COSV57798573;