6-132570483-G-A

Variant names:

• chr6-132570483-G-A
• rs117814299
• NM_175067.1:c.162G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_175067.1(TAAR6):​c.162G>A​(p.Met54Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00396 in 1,613,904 control chromosomes in the GnomAD database, including 210 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0078 (51 hom., cov: 32)
  • Exomes 𝑓: 0.0036 (159 hom.)
• Consequence: TAAR6 NM_175067.1 missense
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.222
• Publications: 6 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0030700862).
• BP6: Variant 6-132570483-G-A is Benign according to our data. Variant chr6-132570483-G-A is described in ClinVar as Benign. ClinVar VariationId is 773730.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.052 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175067.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAAR6	NM_175067.1	MANE Select	c.162G>A	p.Met54Ile	missense	Exon 1 of 1	NP_778237.1	Q96RI8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAAR6	ENST00000275198.1	TSL:6 MANE Select	c.162G>A	p.Met54Ile	missense	Exon 1 of 1	ENSP00000275198.1	Q96RI8

Frequencies

GnomAD3 genomes AF: 0.00776 AC: 1179 AN: 151946 Hom.: 49 Cov.: 32

Gnomad AFR AF: 0.000629

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0509

Gnomad SAS AF: 0.00270

Gnomad FIN AF: 0.000473

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000368

Gnomad OTH AF: 0.00670

GnomAD2 exomes AF: 0.0111 AC: 2779 AN: 251350 AF XY: 0.00910

Gnomad AFR exome AF: 0.000185

Gnomad AMR exome AF: 0.0526

Gnomad ASJ exome AF: 0.000497

Gnomad EAS exome AF: 0.0449

Gnomad FIN exome AF: 0.000554

Gnomad NFE exome AF: 0.000264

Gnomad OTH exome AF: 0.00879

GnomAD4 exome AF: 0.00356 AC: 5206 AN: 1461840 Hom.: 159 Cov.: 31 AF XY: 0.00330 AC XY: 2398 AN XY: 727226

African (AFR) AF: 0.000508 AC: 17 AN: 33478

American (AMR) AF: 0.0534 AC: 2389 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.000383 AC: 10 AN: 26136

East Asian (EAS) AF: 0.0530 AC: 2105 AN: 39696

South Asian (SAS) AF: 0.00147 AC: 127 AN: 86258

European-Finnish (FIN) AF: 0.000374 AC: 20 AN: 53420

Middle Eastern (MID) AF: 0.000347 AC: 2 AN: 5768

European-Non Finnish (NFE) AF: 0.000193 AC: 215 AN: 1111966

Other (OTH) AF: 0.00531 AC: 321 AN: 60396

GnomAD4 genome AF: 0.00779 AC: 1185 AN: 152064 Hom.: 51 Cov.: 32 AF XY: 0.00977 AC XY: 726 AN XY: 74316

African (AFR) AF: 0.000627 AC: 26 AN: 41480

American (AMR) AF: 0.0551 AC: 841 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.0508 AC: 262 AN: 5160

South Asian (SAS) AF: 0.00271 AC: 13 AN: 4802

European-Finnish (FIN) AF: 0.000473 AC: 5 AN: 10578

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000368 AC: 25 AN: 68000

Other (OTH) AF: 0.00616 AC: 13 AN: 2110

Alfa AF: 0.00262 Hom.: 13

Bravo AF: 0.0104

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000778 AC: 3

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.000698 AC: 6

ExAC AF: 0.00811 AC: 985

Asia WGS AF: 0.0260 AC: 89 AN: 3478

EpiCase AF: 0.000382

EpiControl AF: 0.000415

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Benign	-0.51	T
BayesDel_noAF	Benign	-0.46
CADD	Benign	9.4
DANN	Benign	0.49
DEOGEN2	Benign	0.0073	T
Eigen	Benign	-0.93
Eigen_PC	Benign	-0.77
FATHMM_MKL	Benign	0.35	N
LIST_S2	Benign	0.84	T
MetaRNN	Benign	0.0031	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.80	N
PhyloP100		0.22
PrimateAI	Benign	0.31	T
PROVEAN	Benign	0.54	N
REVEL	Benign	0.12
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
Polyphen		0.0	B
Vest4		0.22
MutPred		0.41		Loss of sheet (P = 0.0817)
MPC		0.0094
ClinPred		0.0068	T
GERP RS		4.1
PromoterAI		-0.042	Neutral
Varity_R		0.33
gMVP		0.058
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs117814299; hg19: chr6-132891622; COSMIC: COSV51585248;