dbSNP rs8192624: TAAR6:p.Val265Ile (chr6-132571114-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_175067.1(TAAR6):c.793G>A(p.Val265Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.079 in 1,613,938 control chromosomes in the GnomAD database, including 5,547 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.076 ( 503 hom., cov: 32)

Exomes 𝑓: 0.079 ( 5044 hom. )

Consequence

TAAR6
NM_175067.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.832

Variant links:

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]

TAAR6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0027578175).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR6	NM_175067.1 link	c.793G>A	p.Val265Ile	missense_variant	Exon 1 of 1	ENST00000275198.1	NP_778237.1	Q96RI8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAAR6	ENST00000275198.1 link	c.793G>A	p.Val265Ile	missense_variant	Exon 1 of 1	6	NM_175067.1	ENSP00000275198.1		Q96RI8

Frequencies

GnomAD3 genomes

AF:

0.0757

AC:

11506

AN:

152060

Hom.:

503

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0605

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.0560

Gnomad ASJ

AF:

0.0418

Gnomad EAS

AF:

0.0139

Gnomad SAS

AF:

0.0742

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0880

Gnomad OTH

AF:

0.0664

GnomAD3 exomes

AF:

0.0730

AC:

18311

AN:

250952

Hom.:

805

AF XY:

0.0757

AC XY:

10267

AN XY:

135630

show subpopulations

Gnomad AFR exome

AF:

0.0616

Gnomad AMR exome

AF:

0.0373

Gnomad ASJ exome

AF:

0.0465

Gnomad EAS exome

AF:

0.0105

Gnomad SAS exome

AF:

0.0817

Gnomad FIN exome

AF:

0.114

Gnomad NFE exome

AF:

0.0872

Gnomad OTH exome

AF:

0.0848

GnomAD4 exome

AF:

0.0794

AC:

116034

AN:

1461760

Hom.:

5044

Cov.:

AF XY:

0.0801

AC XY:

58226

AN XY:

727186

show subpopulations

Gnomad4 AFR exome

AF:

0.0600

Gnomad4 AMR exome

AF:

0.0397

Gnomad4 ASJ exome

AF:

0.0432

Gnomad4 EAS exome

AF:

0.0147

Gnomad4 SAS exome

AF:

0.0824

Gnomad4 FIN exome

AF:

0.116

Gnomad4 NFE exome

AF:

0.0828

Gnomad4 OTH exome

AF:

0.0760

GnomAD4 genome

AF:

0.0756

AC:

11507

AN:

152178

Hom.:

503

Cov.:

AF XY:

0.0761

AC XY:

5665

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.0603

Gnomad4 AMR

AF:

0.0560

Gnomad4 ASJ

AF:

0.0418

Gnomad4 EAS

AF:

0.0141

Gnomad4 SAS

AF:

0.0739

Gnomad4 FIN

AF:

0.116

Gnomad4 NFE

AF:

0.0881

Gnomad4 OTH

AF:

0.0681

Alfa

AF:

0.0785

Hom.:

1230

Bravo

AF:

0.0701

TwinsUK

AF:

0.0766

AC:

284

ALSPAC

AF:

0.0828

AC:

319

ESP6500AA

AF:

0.0629

AC:

277

ESP6500EA

AF:

0.0807

AC:

694

ExAC

AF:

0.0759

AC:

9219

Asia WGS

AF:

0.0410

AC:

143

AN:

3478

EpiCase

AF:

0.0847

EpiControl

AF:

0.0903

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.094

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.72

CADD

Benign

0.024

DANN

Benign

0.61

DEOGEN2

Benign

0.010

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.090

LIST_S2

Benign

0.44

MetaRNN

Benign

0.0028

MetaSVM

Benign

-0.96

MutationAssessor

Benign

0.37

PrimateAI

Benign

0.33

PROVEAN

Benign

-0.60

REVEL

Benign

0.028

Sift

Benign

0.83

Sift4G

Benign

0.94

Polyphen

0.0

Vest4

0.014

MPC

0.0097

ClinPred

0.0022

GERP RS

-6.0

Varity_R

0.037

gMVP

0.018

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over