6-132538470-A-T

Position:

• chr6-132538470-A-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_175057.4(TAAR9):​c.181A>T​(p.Lys61*) variant causes a stop gained change. The variant allele was found at a frequency of 0.26 in 1,612,492 control chromosomes in the GnomAD database, including 55,973 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 0.24 (4717 hom., cov: 30)
  • Exomes 𝑓: 0.26 (51256 hom.)
• Consequence: TAAR9 NM_175057.4 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.89

Genes affected

TAAR9 (HGNC:20977): (trace amine associated receptor 9) TAAR9 is a member of a large family of rhodopsin G protein-coupled receptors (GPCRs, or GPRs). GPCRs contain 7 transmembrane domains and transduce extracellular signals through heterotrimeric G proteins.[supplied by OMIM, Jul 2005]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAAR9	NM_175057.4	c.181A>T	p.Lys61*	stop_gained	1/1	ENST00000434551.3	NP_778227.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAAR9	ENST00000434551.3	c.181A>T	p.Lys61*	stop_gained	1/1	6	NM_175057.4	ENSP00000424607.2

Frequencies

GnomAD3 genomes AF: 0.245 AC: 36923 AN: 150832 Hom.: 4715 Cov.: 30

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.238

GnomAD4 exome AF: 0.262 AC: 382464 AN: 1461542 Hom.: 51256 Cov.: 41 AF XY: 0.260 AC XY: 188982 AN XY: 727056

Gnomad4 AFR exome AF: 0.187

Gnomad4 AMR exome AF: 0.273

Gnomad4 ASJ exome AF: 0.271

Gnomad4 EAS exome AF: 0.119

Gnomad4 SAS exome AF: 0.192

Gnomad4 FIN exome AF: 0.259

Gnomad4 NFE exome AF: 0.274

Gnomad4 OTH exome AF: 0.252

GnomAD4 genome AF: 0.245 AC: 36959 AN: 150950 Hom.: 4717 Cov.: 30 AF XY: 0.243 AC XY: 17898 AN XY: 73596

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.238

Alfa AF: 0.265 Hom.: 4088

Bravo AF: 0.244

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Pathogenic	36
Vest4		0.019

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2842899; hg19: chr6-132859609;