6-132600066-G-C

Variant names:

• chr6-132600066-G-C
• rs4467795
• ENST00000657559.1:n.934C>G

Variant summary

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

The ENST00000657559.1(ENSG00000286663):​n.934C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,974 control chromosomes in the GnomAD database, including 21,378 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 0.52 (21378 hom., cov: 31)
• Consequence: ENSG00000286663 ENST00000657559.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 0 publications found

Genes affected

ENSG00000286663 (HGNC:):

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657559.1. 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.-48+8438C>G		intron	N/A	NP_001376456.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286663	ENST00000657559.1		n.934C>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78492 AN: 151856 Hom.: 21349 Cov.: 31

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.517 AC: 78573 AN: 151974 Hom.: 21378 Cov.: 31 AF XY: 0.513 AC XY: 38122 AN XY: 74268

African (AFR) AF: 0.690 AC: 28604 AN: 41438

American (AMR) AF: 0.393 AC: 5987 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1539 AN: 3468

East Asian (EAS) AF: 0.339 AC: 1751 AN: 5172

South Asian (SAS) AF: 0.517 AC: 2494 AN: 4820

European-Finnish (FIN) AF: 0.444 AC: 4687 AN: 10554

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31960 AN: 67960

Other (OTH) AF: 0.499 AC: 1053 AN: 2112

Alfa AF: 0.488 Hom.: 2216

Bravo AF: 0.515

Asia WGS AF: 0.462 AC: 1606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.24
DANN	Benign	0.40
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4467795; hg19: chr6-132921205;