6-132655303-G-T

Variant names:

• chr6-132655303-G-T
• rs1569651
• NM_138327.4:c.-127+3827C>A

Variant summary

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

The NM_138327.4(TAAR1):​c.-127+3827C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,648 control chromosomes in the GnomAD database, including 14,239 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 0.41 (14239 hom., cov: 31)
• Consequence: TAAR1 NM_138327.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR1	NM_138327.4	c.-127+3827C>A		intron_variant	Intron 1 of 1	ENST00000275216.3	NP_612200.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAAR1	ENST00000275216.3	c.-127+3827C>A		intron_variant	Intron 1 of 1	6	NM_138327.4	ENSP00000275216.1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61707 AN: 151542 Hom.: 14241 Cov.: 31

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.407 AC: 61708 AN: 151648 Hom.: 14239 Cov.: 31 AF XY: 0.406 AC XY: 30047 AN XY: 74054

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.431

Alfa AF: 0.483 Hom.: 22227

Bravo AF: 0.397

Asia WGS AF: 0.235 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.21
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1569651; hg19: chr6-132976442;