rs8192625

Variant summary

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

The NM_175067.1(TAAR6):​c.872G>A​(p.Cys291Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0693 in 1,613,852 control chromosomes in the GnomAD database, including 4,185 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 same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.077 ( 467 hom., cov: 32)
Exomes 𝑓: 0.069 ( 3718 hom. )

Consequence

TAAR6
NM_175067.1 missense

Scores

18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.554
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0021861494).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TAAR6NM_175067.1 linkuse as main transcriptc.872G>A p.Cys291Tyr missense_variant 1/1 ENST00000275198.1 NP_778237.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TAAR6ENST00000275198.1 linkuse as main transcriptc.872G>A p.Cys291Tyr missense_variant 1/1 NM_175067.1 ENSP00000275198 P1

Frequencies

GnomAD3 genomes
AF:
0.0766
AC:
11636
AN:
151984
Hom.:
467
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.103
Gnomad AMI
AF:
0.170
Gnomad AMR
AF:
0.0476
Gnomad ASJ
AF:
0.0280
Gnomad EAS
AF:
0.0127
Gnomad SAS
AF:
0.0631
Gnomad FIN
AF:
0.0802
Gnomad MID
AF:
0.0570
Gnomad NFE
AF:
0.0740
Gnomad OTH
AF:
0.0657
GnomAD3 exomes
AF:
0.0619
AC:
15536
AN:
250970
Hom.:
609
AF XY:
0.0629
AC XY:
8533
AN XY:
135630
show subpopulations
Gnomad AFR exome
AF:
0.104
Gnomad AMR exome
AF:
0.0292
Gnomad ASJ exome
AF:
0.0278
Gnomad EAS exome
AF:
0.00925
Gnomad SAS exome
AF:
0.0697
Gnomad FIN exome
AF:
0.0790
Gnomad NFE exome
AF:
0.0718
Gnomad OTH exome
AF:
0.0652
GnomAD4 exome
AF:
0.0686
AC:
100204
AN:
1461750
Hom.:
3718
Cov.:
32
AF XY:
0.0685
AC XY:
49791
AN XY:
727186
show subpopulations
Gnomad4 AFR exome
AF:
0.108
Gnomad4 AMR exome
AF:
0.0305
Gnomad4 ASJ exome
AF:
0.0246
Gnomad4 EAS exome
AF:
0.0137
Gnomad4 SAS exome
AF:
0.0693
Gnomad4 FIN exome
AF:
0.0817
Gnomad4 NFE exome
AF:
0.0714
Gnomad4 OTH exome
AF:
0.0650
GnomAD4 genome
AF:
0.0766
AC:
11645
AN:
152102
Hom.:
467
Cov.:
32
AF XY:
0.0754
AC XY:
5607
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.103
Gnomad4 AMR
AF:
0.0476
Gnomad4 ASJ
AF:
0.0280
Gnomad4 EAS
AF:
0.0129
Gnomad4 SAS
AF:
0.0623
Gnomad4 FIN
AF:
0.0802
Gnomad4 NFE
AF:
0.0740
Gnomad4 OTH
AF:
0.0674
Alfa
AF:
0.0702
Hom.:
756
Bravo
AF:
0.0730
TwinsUK
AF:
0.0701
AC:
260
ALSPAC
AF:
0.0737
AC:
284
ESP6500AA
AF:
0.103
AC:
456
ESP6500EA
AF:
0.0677
AC:
582
ExAC
AF:
0.0645
AC:
7831
Asia WGS
AF:
0.0510
AC:
175
AN:
3478
EpiCase
AF:
0.0677
EpiControl
AF:
0.0677

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.080
BayesDel_addAF
Benign
-0.72
T
BayesDel_noAF
Benign
-0.72
CADD
Benign
0.53
DANN
Benign
0.18
DEOGEN2
Benign
0.0072
T
Eigen
Benign
-1.6
Eigen_PC
Benign
-1.4
FATHMM_MKL
Benign
0.012
N
LIST_S2
Benign
0.53
T
MetaRNN
Benign
0.0022
T
MetaSVM
Benign
-0.94
T
MutationAssessor
Benign
-1.9
N
MutationTaster
Benign
1.0
N
PrimateAI
Benign
0.35
T
PROVEAN
Benign
3.3
N
REVEL
Benign
0.13
Sift
Benign
1.0
T
Sift4G
Benign
1.0
T
Polyphen
0.0
B
Vest4
0.020
MPC
0.0088
ClinPred
0.0021
T
GERP RS
3.9
Varity_R
0.049
gMVP
0.12

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.

Other links and lift over

dbSNP: rs8192625; hg19: chr6-132892332; COSMIC: COSV51583366; API