chr6-132606363-G-C

Variant names:

• chr6-132606363-G-C
• rs12189813
• NM_001389527.1:c.-48+2141C>G

Variant summary

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

The NM_001389527.1(TAAR5):​c.-48+2141C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,976 control chromosomes in the GnomAD database, including 10,518 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 0.37 (10518 hom., cov: 32)
• Consequence: TAAR5 NM_001389527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 3 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR5	NM_001389527.1	c.-48+2141C>G		intron_variant	Intron 3 of 3		NP_001376456.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55566 AN: 151858 Hom.: 10510 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.366 AC: 55608 AN: 151976 Hom.: 10518 Cov.: 32 AF XY: 0.361 AC XY: 26774 AN XY: 74264

African (AFR) AF: 0.410 AC: 16981 AN: 41450

American (AMR) AF: 0.279 AC: 4253 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1102 AN: 3472

East Asian (EAS) AF: 0.0826 AC: 427 AN: 5172

South Asian (SAS) AF: 0.330 AC: 1585 AN: 4810

European-Finnish (FIN) AF: 0.370 AC: 3906 AN: 10544

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26316 AN: 67948

Other (OTH) AF: 0.351 AC: 742 AN: 2114

Alfa AF: 0.364 Hom.: 1245

Bravo AF: 0.356

Asia WGS AF: 0.204 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.31
DANN	Benign	0.38
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12189813; hg19: chr6-132927502;