6-132571367-T-G

Variant names:

• chr6-132571367-T-G
• rs7772821
• NM_175067.1:c.*8T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000275198.1(TAAR6):​c.*8T>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. 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: TAAR6 ENST00000275198.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95
• Publications: 14 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000275198.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAAR6	NM_175067.1	MANE Select	c.*8T>G		downstream_gene	N/A	NP_778237.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAAR6	ENST00000275198.1	TSL:6 MANE Select	c.*8T>G		downstream_gene	N/A	ENSP00000275198.1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45450 AN: 151950 Hom.: 9835 Cov.: 32

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

GnomAD2 exomes AF: 0.225 AC: 49847 AN: 221168 AF XY: 0.218

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 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.: 32 AF XY: 0.182 AC XY: 128835 AN XY: 708154

African (AFR) AF: 0.628 AC: 20156 AN: 32076

American (AMR) AF: 0.270 AC: 10433 AN: 38690

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 4272 AN: 24162

East Asian (EAS) AF: 0.210 AC: 8269 AN: 39372

South Asian (SAS) AF: 0.251 AC: 20135 AN: 80154

European-Finnish (FIN) AF: 0.135 AC: 7047 AN: 52326

Middle Eastern (MID) AF: 0.293 AC: 1586 AN: 5404

European-Non Finnish (NFE) AF: 0.160 AC: 175105 AN: 1097528

Other (OTH) AF: 0.203 AC: 11924 AN: 58880

GnomAD4 genome AF: 0.299 AC: 45537 AN: 152068 Hom.: 9862 Cov.: 32 AF XY: 0.296 AC XY: 21991 AN XY: 74346

African (AFR) AF: 0.614 AC: 25447 AN: 41436

American (AMR) AF: 0.249 AC: 3810 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 572 AN: 3472

East Asian (EAS) AF: 0.207 AC: 1074 AN: 5192

South Asian (SAS) AF: 0.252 AC: 1212 AN: 4814

European-Finnish (FIN) AF: 0.129 AC: 1363 AN: 10580

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11101 AN: 67982

Other (OTH) AF: 0.291 AC: 615 AN: 2112

Alfa AF: 0.219 Hom.: 13160

Bravo AF: 0.324

Asia WGS AF: 0.244 AC: 849 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.098
DANN	Benign	0.34
PhyloP100		-2.9
Mutation Taster		=79/21	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7772821; hg19: chr6-132892506; COSMIC: COSV51583221;