rs9389011

Variant names:

• chr6-132613440-T-C
• rs9389011
• NM_001389527.1:c.-323+3260A>G

Variant summary

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

The NM_001389527.1(TAAR5):​c.-323+3260A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,144 control chromosomes in the GnomAD database, including 2,860 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 (2860 hom., cov: 32)
• Consequence: TAAR5 NM_001389527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR5	NM_001389527.1	c.-323+3260A>G		intron_variant	Intron 1 of 3		NP_001376456.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26413 AN: 152026 Hom.: 2861 Cov.: 32

Gnomad AFR AF: 0.0492

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.173 AC: 26397 AN: 152144 Hom.: 2860 Cov.: 32 AF XY: 0.176 AC XY: 13084 AN XY: 74376

Gnomad4 AFR AF: 0.0491

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.166

Alfa AF: 0.211 Hom.: 3735

Bravo AF: 0.164

Asia WGS AF: 0.235 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.8
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9389011; hg19: chr6-132934579;