rs1081074

Variant names:

• chr6-132610318-C-A
• rs1081074
• NM_001389527.1:c.-322-957G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001389527.1(TAAR5):​c.-322-957G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,142 control chromosomes in the GnomAD database, including 3,304 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 0.13 (3304 hom., cov: 32)
• Consequence: TAAR5 NM_001389527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71
• Publications: 0 publications found

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]

ENSG00000290584 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.385 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001389527.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAAR5	NM_001389527.1		c.-322-957G>T		intron	N/A	NP_001376456.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290584	ENST00000466706.2	TSL:6	n.217-957G>T		intron	N/A
	ENSG00000290584	ENST00000837004.1		n.201-957G>T		intron	N/A
	ENSG00000290584	ENST00000837005.1		n.145-957G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19095 AN: 152024 Hom.: 3287 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0658

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.0968

Gnomad SAS AF: 0.0678

Gnomad FIN AF: 0.0131

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0104

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.126 AC: 19149 AN: 152142 Hom.: 3304 Cov.: 32 AF XY: 0.124 AC XY: 9198 AN XY: 74390

African (AFR) AF: 0.390 AC: 16172 AN: 41454

American (AMR) AF: 0.0657 AC: 1003 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3470

East Asian (EAS) AF: 0.0974 AC: 504 AN: 5176

South Asian (SAS) AF: 0.0674 AC: 326 AN: 4834

European-Finnish (FIN) AF: 0.0131 AC: 139 AN: 10620

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0104 AC: 709 AN: 68004

Other (OTH) AF: 0.106 AC: 224 AN: 2106

Alfa AF: 0.0421 Hom.: 1716

Bravo AF: 0.142

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.14
DANN	Benign	0.23
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs1081074; hg19: chr6-132931457;