Variant 6-132570483-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_175067.1(TAAR6):c.162G>A(p.Met54Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00396 in 1,613,904 control chromosomes in the GnomAD database, including 210 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0078 ( 51 hom., cov: 32)

Exomes 𝑓: 0.0036 ( 159 hom. )

Consequence

TAAR6
NM_175067.1 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.222

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0030700862).

BP6

Variant 6-132570483-G-A is Benign according to our data. Variant chr6-132570483-G-A is described in ClinVar as [Benign]. Clinvar id is 773730.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.052 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAAR6	NM_175067.1 linkuse as main transcript	c.162G>A	p.Met54Ile	missense_variant	1/1	ENST00000275198.1	NP_778237.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAAR6	ENST00000275198.1 linkuse as main transcript	c.162G>A	p.Met54Ile	missense_variant	1/1		NM_175067.1	ENSP00000275198	P1

Frequencies

GnomAD3 genomes

AF:

0.00776

AC:

1179

AN:

151946

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000629

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0547

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0509

Gnomad SAS

AF:

0.00270

Gnomad FIN

AF:

0.000473

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000368

Gnomad OTH

AF:

0.00670

GnomAD3 exomes

AF:

0.0111

AC:

2779

AN:

251350

Hom.:

AF XY:

0.00910

AC XY:

1236

AN XY:

135840

show subpopulations

Gnomad AFR exome

AF:

0.000185

Gnomad AMR exome

AF:

0.0526

Gnomad ASJ exome

AF:

0.000497

Gnomad EAS exome

AF:

0.0449

Gnomad SAS exome

AF:

0.00105

Gnomad FIN exome

AF:

0.000554

Gnomad NFE exome

AF:

0.000264

Gnomad OTH exome

AF:

0.00879

GnomAD4 exome

AF:

0.00356

AC:

5206

AN:

1461840

Hom.:

159

Cov.:

AF XY:

0.00330

AC XY:

2398

AN XY:

727226

show subpopulations

Gnomad4 AFR exome

AF:

0.000508

Gnomad4 AMR exome

AF:

0.0534

Gnomad4 ASJ exome

AF:

0.000383

Gnomad4 EAS exome

AF:

0.0530

Gnomad4 SAS exome

AF:

0.00147

Gnomad4 FIN exome

AF:

0.000374

Gnomad4 NFE exome

AF:

0.000193

Gnomad4 OTH exome

AF:

0.00531

GnomAD4 genome

AF:

0.00779

AC:

1185

AN:

152064

Hom.:

Cov.:

AF XY:

0.00977

AC XY:

726

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.000627

Gnomad4 AMR

AF:

0.0551

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0508

Gnomad4 SAS

AF:

0.00271

Gnomad4 FIN

AF:

0.000473

Gnomad4 NFE

AF:

0.000368

Gnomad4 OTH

AF:

0.00616

Alfa

AF:

0.00196

Hom.:

Bravo

AF:

0.0104

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000778

AC:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.000698

AC:

ExAC

AF:

0.00811

AC:

985

Asia WGS

AF:

0.0260

AC:

AN:

3478

EpiCase

AF:

0.000382

EpiControl

AF:

0.000415

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Apr 07, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.46

CADD

Benign

9.4

DANN

Benign

0.49

DEOGEN2

Benign

0.0073

Eigen

Benign

-0.93

Eigen_PC

Benign

-0.77

FATHMM_MKL

Benign

0.35

LIST_S2

Benign

0.84

MetaRNN

Benign

0.0031

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.80

MutationTaster

Benign

0.98

PrimateAI

Benign

0.31

PROVEAN

Benign

0.54

REVEL

Benign

0.12

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.22

MutPred

0.41

Loss of sheet (P = 0.0817);

MPC

0.0094

ClinPred

0.0068

GERP RS

4.1

Varity_R

0.33

gMVP

0.058

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over