rs4421218

Variant names:

• chr6-132609953-C-T
• rs4421218
• NM_001389527.1:c.-322-592G>A

Variant summary

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

The NM_001389527.1(TAAR5):​c.-322-592G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0445 in 149,772 control chromosomes in the GnomAD database, including 198 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 0.045 (198 hom., cov: 32)
• Consequence: TAAR5 NM_001389527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR5	NM_001389527.1	c.-322-592G>A		intron_variant	Intron 1 of 3		NP_001376456.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290584	ENST00000466706.2	n.217-592G>A		intron_variant	Intron 2 of 2	6
ENSG00000290584	ENST00000837004.1	n.201-592G>A		intron_variant	Intron 1 of 1
ENSG00000290584	ENST00000837005.1	n.145-592G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0445 AC: 6662 AN: 149654 Hom.: 199 Cov.: 32

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.00661

Gnomad AMR AF: 0.0715

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0850

Gnomad FIN AF: 0.0602

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0284

Gnomad OTH AF: 0.0426

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

GnomAD4 genome AF: 0.0445 AC: 6671 AN: 149772 Hom.: 198 Cov.: 32 AF XY: 0.0488 AC XY: 3569 AN XY: 73122

African (AFR) AF: 0.0493 AC: 1957 AN: 39706

American (AMR) AF: 0.0713 AC: 1076 AN: 15088

Ashkenazi Jewish (ASJ) AF: 0.0136 AC: 47 AN: 3454

East Asian (EAS) AF: 0.101 AC: 518 AN: 5132

South Asian (SAS) AF: 0.0857 AC: 405 AN: 4724

European-Finnish (FIN) AF: 0.0602 AC: 635 AN: 10548

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.0284 AC: 1930 AN: 67854

Other (OTH) AF: 0.0431 AC: 89 AN: 2066

Alfa AF: 0.0333 Hom.: 17

Bravo AF: 0.0428

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.1
DANN	Benign	0.61
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs4421218; hg19: chr6-132931092;