NM_175067.1:c.-240A>C

Variant names:

• chr6-132570082-A-C
• rs17061449
• NM_175067.1:c.-240A>C

Variant summary

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

The NM_175067.1(TAAR6):​c.-240A>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.07 in 152,316 control chromosomes in the GnomAD database, including 387 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 0.070 (387 hom., cov: 32)
• Consequence: TAAR6 NM_175067.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 0 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR6	NM_175067.1	c.-240A>C		upstream_gene_variant		ENST00000275198.1	NP_778237.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAAR6	ENST00000275198.1	c.-240A>C		upstream_gene_variant		6	NM_175067.1	ENSP00000275198.1

Frequencies

GnomAD3 genomes AF: 0.0700 AC: 10655 AN: 152198 Hom.: 386 Cov.: 32

Gnomad AFR AF: 0.0699

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0792

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.0304

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.0640

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0769

Gnomad OTH AF: 0.0751

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0700 AC: 10665 AN: 152316 Hom.: 387 Cov.: 32 AF XY: 0.0684 AC XY: 5091 AN XY: 74472

African (AFR) AF: 0.0700 AC: 2908 AN: 41568

American (AMR) AF: 0.0791 AC: 1209 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0392 AC: 136 AN: 3472

East Asian (EAS) AF: 0.0305 AC: 158 AN: 5188

South Asian (SAS) AF: 0.0180 AC: 87 AN: 4832

European-Finnish (FIN) AF: 0.0640 AC: 679 AN: 10610

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0769 AC: 5234 AN: 68040

Other (OTH) AF: 0.0734 AC: 155 AN: 2112

Alfa AF: 0.0749 Hom.: 71

Bravo AF: 0.0740

Asia WGS AF: 0.0270 AC: 95 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.0
DANN	Benign	0.64
PhyloP100		0.25
PromoterAI		-0.00030	Neutral

Splicing

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

Other links and lift over

dbSNP: rs17061449; hg19: chr6-132891221;