rs4897595

Variant names:

• chr6-132646232-G-A
• rs4897595
• NM_138327.4:c.-126-103C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138327.4. 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
	TAAR1	NM_138327.4	MANE Select	c.-126-103C>T		intron	N/A	NP_612200.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAAR1	ENST00000275216.3	TSL:6 MANE Select	c.-126-103C>T		intron	N/A	ENSP00000275216.1

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

African (AFR) AF: 0.0593 AC: 2463 AN: 41504

American (AMR) AF: 0.0778 AC: 1189 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0219 AC: 76 AN: 3470

East Asian (EAS) AF: 0.112 AC: 578 AN: 5180

South Asian (SAS) AF: 0.0887 AC: 428 AN: 4824

European-Finnish (FIN) AF: 0.0752 AC: 796 AN: 10588

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0562 AC: 3817 AN: 67974

Other (OTH) AF: 0.0531 AC: 112 AN: 2108

Alfa AF: 0.0613 Hom.: 34

Bravo AF: 0.0594

Asia WGS AF: 0.0810 AC: 280 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.8
DANN	Benign	0.25
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs4897595; hg19: chr6-132967371;