Variant 6-132571367-T-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The variant allele was found at a frequency of 0.193 in 1,580,660 control chromosomes in the GnomAD database, including 37,748 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 0.30 ( 9862 hom., cov: 32)

Exomes 𝑓: 0.18 ( 27886 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.95

Variant links:

Genes affected

(HGNC:):

links:

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 (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.132571367T>G		intergenic_region
TAAR6	NM_175067.1 linkuse as main transcript	c.*8T>G		downstream_gene_variant		ENST00000275198.1	NP_778237.1	Q96RI8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAAR6	ENST00000275198.1 linkuse as main transcript	c.*8T>G		downstream_gene_variant		6	NM_175067.1	ENSP00000275198.1		Q96RI8

Frequencies

GnomAD3 genomes

AF:

0.299

AC:

45450

AN:

151950

Hom.:

9835

Cov.:

show subpopulations

Gnomad AFR

AF:

0.614

Gnomad AMI

AF:

0.293

Gnomad AMR

AF:

0.249

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.207

Gnomad SAS

AF:

0.252

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.163

Gnomad OTH

AF:

0.289

GnomAD3 exomes

AF:

0.225

AC:

49847

AN:

221168

Hom.:

7070

AF XY:

0.218

AC XY:

26145

AN XY:

119734

show subpopulations

Gnomad AFR exome

AF:

0.619

Gnomad AMR exome

AF:

0.280

Gnomad ASJ exome

AF:

0.189

Gnomad EAS exome

AF:

0.199

Gnomad SAS exome

AF:

0.262

Gnomad FIN exome

AF:

0.132

Gnomad NFE exome

AF:

0.169

Gnomad OTH exome

AF:

0.211

GnomAD4 exome

AF:

0.181

AC:

258927

AN:

1428592

Hom.:

27886

Cov.:

AF XY:

0.182

AC XY:

128835

AN XY:

708154

show subpopulations

Gnomad4 AFR exome

AF:

0.628

Gnomad4 AMR exome

AF:

0.270

Gnomad4 ASJ exome

AF:

0.177

Gnomad4 EAS exome

AF:

0.210

Gnomad4 SAS exome

AF:

0.251

Gnomad4 FIN exome

AF:

0.135

Gnomad4 NFE exome

AF:

0.160

Gnomad4 OTH exome

AF:

0.203

GnomAD4 genome

AF:

0.299

AC:

45537

AN:

152068

Hom.:

9862

Cov.:

AF XY:

0.296

AC XY:

21991

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.614

Gnomad4 AMR

AF:

0.249

Gnomad4 ASJ

AF:

0.165

Gnomad4 EAS

AF:

0.207

Gnomad4 SAS

AF:

0.252

Gnomad4 FIN

AF:

0.129

Gnomad4 NFE

AF:

0.163

Gnomad4 OTH

AF:

0.291

Alfa

AF:

0.206

Hom.:

4126

Bravo

AF:

0.324

Asia WGS

AF:

0.244

AC:

849

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.098

DANN

Benign

0.34

Splicing

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