rs4421218

chr6-132609953-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

TAAR5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TAAR5	NM_001389527.1	c.-322-592G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0493

Gnomad4 AMR AF: 0.0713

Gnomad4 ASJ AF: 0.0136

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0857

Gnomad4 FIN AF: 0.0602

Gnomad4 NFE AF: 0.0284

Gnomad4 OTH AF: 0.0431

Alfa AF: 0.0328 Hom.: 16

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4421218; hg19: chr6-132931092;