chr6-132570399-C-T

Position:

• chr6-132570399-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_175067.1(TAAR6):​c.78C>T​(p.Pro26Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0464 in 1,614,040 control chromosomes in the GnomAD database, including 2,001 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 0.037 (151 hom., cov: 32)
  • Exomes 𝑓: 0.047 (1850 hom.)
• Consequence: TAAR6 NM_175067.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

TAAR6 (HGNC:20978): (trace amine associated receptor 6) This gene encodes a seven-transmembrane G-protein-coupled receptor that likely functions as a receptor for endogenous trace amines. Mutations in this gene may be associated with schizophrenia.[provided by RefSeq, Feb 2010]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BP7: Synonymous conserved (PhyloP=-1.09 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAAR6	NM_175067.1	c.78C>T	p.Pro26Pro	synonymous_variant	1/1	ENST00000275198.1	NP_778237.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAAR6	ENST00000275198.1	c.78C>T	p.Pro26Pro	synonymous_variant	1/1	6	NM_175067.1	ENSP00000275198.1

Frequencies

GnomAD3 genomes AF: 0.0369 AC: 5612 AN: 152122 Hom.: 151 Cov.: 32

Gnomad AFR AF: 0.00869

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0225

Gnomad ASJ AF: 0.0181

Gnomad EAS AF: 0.00847

Gnomad SAS AF: 0.0323

Gnomad FIN AF: 0.0627

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0556

Gnomad OTH AF: 0.0320

GnomAD3 exomes AF: 0.0394 AC: 9880 AN: 250990 Hom.: 257 AF XY: 0.0410 AC XY: 5559 AN XY: 135670

Gnomad AFR exome AF: 0.00911

Gnomad AMR exome AF: 0.0166

Gnomad ASJ exome AF: 0.0178

Gnomad EAS exome AF: 0.00572

Gnomad SAS exome AF: 0.0353

Gnomad FIN exome AF: 0.0623

Gnomad NFE exome AF: 0.0544

Gnomad OTH exome AF: 0.0454

GnomAD4 exome AF: 0.0474 AC: 69329 AN: 1461800 Hom.: 1850 Cov.: 31 AF XY: 0.0474 AC XY: 34491 AN XY: 727200

Gnomad4 AFR exome AF: 0.00809

Gnomad4 AMR exome AF: 0.0175

Gnomad4 ASJ exome AF: 0.0173

Gnomad4 EAS exome AF: 0.00925

Gnomad4 SAS exome AF: 0.0341

Gnomad4 FIN exome AF: 0.0651

Gnomad4 NFE exome AF: 0.0524

Gnomad4 OTH exome AF: 0.0422

GnomAD4 genome AF: 0.0369 AC: 5616 AN: 152240 Hom.: 151 Cov.: 32 AF XY: 0.0363 AC XY: 2699 AN XY: 74432

Gnomad4 AFR AF: 0.00866

Gnomad4 AMR AF: 0.0226

Gnomad4 ASJ AF: 0.0181

Gnomad4 EAS AF: 0.00849

Gnomad4 SAS AF: 0.0324

Gnomad4 FIN AF: 0.0627

Gnomad4 NFE AF: 0.0556

Gnomad4 OTH AF: 0.0340

Alfa AF: 0.0457 Hom.: 141

Bravo AF: 0.0321

Asia WGS AF: 0.0200 AC: 70 AN: 3476

EpiCase AF: 0.0497

EpiControl AF: 0.0523

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.6
DANN	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs8192622; hg19: chr6-132891538;