rs4897595

Positions:

• chr6-132646232-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138327.4(TAAR1):​c.-126-103C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0624 in 152,128 control chromosomes in the GnomAD database, including 337 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 0.062 (337 hom., cov: 32)
• Consequence: TAAR1 NM_138327.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296

Genes affected

TAAR1 (HGNC:17734): (trace amine associated receptor 1) The protein encoded by this gene is a G-protein coupled receptor activated by trace amines. The encoded protein responds little or not at all to dopamine, serotonin, epinephrine, or histamine, but responds well to beta-phenylethylamine, p-tyramine, octopamine, and tryptamine. While primarily functioning in neurologic systems, there is evidence that this gene is involved in blood cell and immunologic functions as well. This gene is thought to be intronless. [provided by RefSeq, Nov 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAAR1	NM_138327.4	c.-126-103C>T		intron_variant		ENST00000275216.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAAR1	ENST00000275216.3	c.-126-103C>T		intron_variant			NM_138327.4	P1

Frequencies

GnomAD3 genomes AF: 0.0623 AC: 9471 AN: 152008 Hom.: 336 Cov.: 32

Gnomad AFR AF: 0.0591

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0780

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0870

Gnomad FIN AF: 0.0752

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0561

Gnomad OTH AF: 0.0532

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

GnomAD4 genome AF: 0.0624 AC: 9489 AN: 152128 Hom.: 337 Cov.: 32 AF XY: 0.0650 AC XY: 4830 AN XY: 74362

Gnomad4 AFR AF: 0.0593

Gnomad4 AMR AF: 0.0778

Gnomad4 ASJ AF: 0.0219

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0887

Gnomad4 FIN AF: 0.0752

Gnomad4 NFE AF: 0.0562

Gnomad4 OTH AF: 0.0531

Alfa AF: 0.0614 Hom.: 32

Bravo AF: 0.0594

Asia WGS AF: 0.0810 AC: 280 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.8
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4897595; hg19: chr6-132967371;