Variant 6-132589104-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_003967.3(TAAR5):c.583C>A(p.Leu195Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00553 in 1,613,932 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0041 ( 2 hom., cov: 31)

Exomes 𝑓: 0.0057 ( 32 hom. )

Consequence

TAAR5
NM_003967.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.880

Variant links:

Genes affected

TAAR5 (HGNC:30236): (trace amine associated receptor 5) Enables trimethylamine receptor activity. Predicted to be involved in signal transduction. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

TAAR5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.009095699).

BP6

Variant 6-132589104-G-T is Benign according to our data. Variant chr6-132589104-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2656916.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAAR5	NM_003967.3 linkuse as main transcript	c.583C>A	p.Leu195Met	missense_variant	1/1	ENST00000258034.4
TAAR5	NM_001389527.1 linkuse as main transcript	c.583C>A	p.Leu195Met	missense_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAAR5	ENST00000258034.4 linkuse as main transcript	c.583C>A	p.Leu195Met	missense_variant	1/1		NM_003967.3	P1

Frequencies

GnomAD3 genomes

AF:

0.00409

AC:

622

AN:

152176

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000989

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00471

Gnomad ASJ

AF:

0.0205

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00104

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00609

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00447

AC:

1118

AN:

250332

Hom.:

AF XY:

0.00458

AC XY:

621

AN XY:

135504

show subpopulations

Gnomad AFR exome

AF:

0.000741

Gnomad AMR exome

AF:

0.00338

Gnomad ASJ exome

AF:

0.0202

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000262

Gnomad FIN exome

AF:

0.00222

Gnomad NFE exome

AF:

0.00616

Gnomad OTH exome

AF:

0.00573

GnomAD4 exome

AF:

0.00568

AC:

8297

AN:

1461638

Hom.:

Cov.:

AF XY:

0.00552

AC XY:

4012

AN XY:

727132

show subpopulations

Gnomad4 AFR exome

AF:

0.000687

Gnomad4 AMR exome

AF:

0.00371

Gnomad4 ASJ exome

AF:

0.0193

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000267

Gnomad4 FIN exome

AF:

0.00221

Gnomad4 NFE exome

AF:

0.00639

Gnomad4 OTH exome

AF:

0.00547

GnomAD4 genome

AF:

0.00409

AC:

623

AN:

152294

Hom.:

Cov.:

AF XY:

0.00384

AC XY:

286

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.000986

Gnomad4 AMR

AF:

0.00471

Gnomad4 ASJ

AF:

0.0205

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00104

Gnomad4 NFE

AF:

0.00610

Gnomad4 OTH

AF:

0.00425

Alfa

AF:

0.00676

Hom.:

Bravo

AF:

0.00441

TwinsUK

AF:

0.00566

AC:

ALSPAC

AF:

0.00830

AC:

ESP6500AA

AF:

0.00114

AC:

ESP6500EA

AF:

0.00663

AC:

ExAC

AF:

0.00428

AC:

519

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

TAAR5: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.19

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.49

Cadd

Benign

Dann

Uncertain

0.99

DEOGEN2

Benign

0.0070

Eigen

Benign

-0.16

Eigen_PC

Benign

-0.23

FATHMM_MKL

Benign

0.12

LIST_S2

Benign

0.61

M_CAP

Benign

0.0043

MetaRNN

Benign

0.0091

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.3

MutationTaster

Benign

1.0

PrimateAI

Benign

0.31

PROVEAN

Benign

-0.080

REVEL

Benign

0.14

Sift

Benign

0.30

Sift4G

Benign

0.30

Polyphen

1.0

Vest4

0.41

MVP

0.69

MPC

0.073

ClinPred

0.033

GERP RS

2.7

Varity_R

0.19

gMVP

0.29

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over