rs4144146

Positions:

• chr6-132595254-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001389527.1(TAAR5):​c.-47-5521C>T variant causes a intron change. The variant allele was found at a frequency of 0.144 in 153,460 control chromosomes in the GnomAD database, including 2,142 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 (2138 hom., cov: 31)
  • Exomes 𝑓: 0.043 (4 hom.)
• Consequence: TAAR5 NM_001389527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.28

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]

TAAR4P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAAR5	NM_001389527.1	c.-47-5521C>T		intron_variant			NP_001376456.1
TAAR4P		n.132595254G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAAR4P	ENST00000454843.1	n.183C>T		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22009 AN: 151956 Hom.: 2136 Cov.: 31

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0804

Gnomad OTH AF: 0.143

GnomAD4 exome AF: 0.0433 AC: 60 AN: 1386 Hom.: 4 Cov.: 0 AF XY: 0.0450 AC XY: 36 AN XY: 800

Gnomad4 AFR exome AF: 0.286

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.167

Gnomad4 SAS exome AF: 0.333

Gnomad4 FIN exome AF: 0.0245

Gnomad4 NFE exome AF: 0.0500

Gnomad4 OTH exome AF: 0.146

GnomAD4 genome AF: 0.145 AC: 22036 AN: 152074 Hom.: 2138 Cov.: 31 AF XY: 0.146 AC XY: 10881 AN XY: 74338

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.0717

Gnomad4 NFE AF: 0.0803

Gnomad4 OTH AF: 0.144

Alfa AF: 0.114 Hom.: 509

Bravo AF: 0.153

Asia WGS AF: 0.231 AC: 801 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	15
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4144146; hg19: chr6-132916393;