Genetic Variant NM_175057.4:c.181A>T (chr6-132538470-A-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_175057.4(TAAR9):c.181A>T(p.Lys61*) variant causes a stop gained change. The variant allele was found at a frequency of 0.26 in 1,612,492 control chromosomes in the GnomAD database, including 55,973 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 0.24 ( 4717 hom., cov: 30)

Exomes 𝑓: 0.26 ( 51256 hom. )

Consequence

TAAR9
NM_175057.4 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.89

Publications

25 publications found

Variant links:

Genes affected

TAAR9 (HGNC:20977): (trace amine associated receptor 9) TAAR9 is a member of a large family of rhodopsin G protein-coupled receptors (GPCRs, or GPRs). GPCRs contain 7 transmembrane domains and transduce extracellular signals through heterotrimeric G proteins.[supplied by OMIM, Jul 2005]

TAAR9 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR9	NM_175057.4 link	c.181A>T	p.Lys61*	stop_gained	Exon 1 of 1	ENST00000434551.3	NP_778227.3	Q96RI9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAAR9	ENST00000434551.3 link	c.181A>T	p.Lys61*	stop_gained	Exon 1 of 1	6	NM_175057.4	ENSP00000424607.2		Q96RI9

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

36923

AN:

150832

Hom.:

4715

Cov.:

show subpopulations

Gnomad AFR

AF:

0.190

Gnomad AMI

AF:

0.384

Gnomad AMR

AF:

0.281

Gnomad ASJ

AF:

0.269

Gnomad EAS

AF:

0.118

Gnomad SAS

AF:

0.194

Gnomad FIN

AF:

0.261

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.277

Gnomad OTH

AF:

0.238

GnomAD4 exome

AF:

0.262

AC:

382464

AN:

1461542

Hom.:

51256

Cov.:

AF XY:

0.260

AC XY:

188982

AN XY:

727056

show subpopulations

African (AFR)

AF:

0.187

AC:

6258

AN:

33464

American (AMR)

AF:

0.273

AC:

12218

AN:

44680

Ashkenazi Jewish (ASJ)

AF:

0.271

AC:

7091

AN:

26130

East Asian (EAS)

AF:

0.119

AC:

4705

AN:

39698

South Asian (SAS)

AF:

0.192

AC:

16558

AN:

86258

European-Finnish (FIN)

AF:

0.259

AC:

13809

AN:

53400

Middle Eastern (MID)

AF:

0.272

AC:

1567

AN:

5766

European-Non Finnish (NFE)

AF:

0.274

AC:

305023

AN:

1111780

Other (OTH)

AF:

0.252

AC:

15235

AN:

60366

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

19628

39255

58883

78510

98138

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10076

20152

30228

40304

50380

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.245

AC:

36959

AN:

150950

Hom.:

4717

Cov.:

AF XY:

0.243

AC XY:

17898

AN XY:

73596

show subpopulations

African (AFR)

AF:

0.190

AC:

7809

AN:

41114

American (AMR)

AF:

0.281

AC:

4249

AN:

15112

Ashkenazi Jewish (ASJ)

AF:

0.269

AC:

933

AN:

3466

East Asian (EAS)

AF:

0.118

AC:

598

AN:

5070

South Asian (SAS)

AF:

0.195

AC:

928

AN:

4768

European-Finnish (FIN)

AF:

0.261

AC:

2689

AN:

10296

Middle Eastern (MID)

AF:

0.293

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.277

AC:

18822

AN:

67836

Other (OTH)

AF:

0.238

AC:

496

AN:

2086

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1392

2784

4176

5568

6960

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

384

768

1152

1536

1920

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.265

Hom.:

4088

Bravo

AF:

0.244

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Pathogenic

(source)

PhyloP100

4.9

Vest4

0.019

PromoterAI

-0.017

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over