dbSNP rs17010664: TACR1:c.*269A>G (chr2-75049163-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001058.4(TACR1):c.*269A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 436,248 control chromosomes in the GnomAD database, including 4,170 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 0.14 ( 1815 hom., cov: 33)

Exomes 𝑓: 0.12 ( 2355 hom. )

Consequence

TACR1
NM_001058.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.455

Publications

6 publications found

Variant links:

Genes affected

TACR1 (HGNC:11526): (tachykinin receptor 1) This gene belongs to a gene family of tachykinin receptors. These tachykinin receptors are characterized by interactions with G proteins and contain seven hydrophobic transmembrane regions. This gene encodes the receptor for the tachykinin substance P, also referred to as neurokinin 1. The encoded protein is also involved in the mediation of phosphatidylinositol metabolism of substance P. [provided by RefSeq, Sep 2008]

TACR1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001058.4. 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
	TACR1	NM_001058.4	MANE Select	c.*269A>G		3_prime_UTR	Exon 5 of 5	NP_001049.1	P25103-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR1	ENST00000305249.10	TSL:1 MANE Select	c.*269A>G		3_prime_UTR	Exon 5 of 5	ENSP00000303522.4	P25103-1

Frequencies

GnomAD3 genomes

AF:

0.143

AC:

21720

AN:

152038

Hom.:

1804

Cov.:

show subpopulations

Gnomad AFR

AF:

0.182

Gnomad AMI

AF:

0.171

Gnomad AMR

AF:

0.175

Gnomad ASJ

AF:

0.0585

Gnomad EAS

AF:

0.00445

Gnomad SAS

AF:

0.0395

Gnomad FIN

AF:

0.234

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.111

GnomAD4 exome

AF:

0.115

AC:

32806

AN:

284092

Hom.:

2355

Cov.:

AF XY:

0.112

AC XY:

16351

AN XY:

145504

show subpopulations

African (AFR)

AF:

0.171

AC:

1609

AN:

9426

American (AMR)

AF:

0.213

AC:

2196

AN:

10298

Ashkenazi Jewish (ASJ)

AF:

0.0667

AC:

643

AN:

9646

East Asian (EAS)

AF:

0.00396

AC:

AN:

21702

South Asian (SAS)

AF:

0.0423

AC:

766

AN:

18120

European-Finnish (FIN)

AF:

0.214

AC:

4082

AN:

19082

Middle Eastern (MID)

AF:

0.0431

AC:

AN:

1392

European-Non Finnish (NFE)

AF:

0.120

AC:

21304

AN:

176872

Other (OTH)

AF:

0.117

AC:

2060

AN:

17554

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1321

2643

3964

5286

6607

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

138

276

414

552

690

<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:

0.143

AC:

21779

AN:

152156

Hom.:

1815

Cov.:

AF XY:

0.146

AC XY:

10892

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.183

AC:

7603

AN:

41502

American (AMR)

AF:

0.175

AC:

2678

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0585

AC:

203

AN:

3470

East Asian (EAS)

AF:

0.00465

AC:

AN:

5162

South Asian (SAS)

AF:

0.0398

AC:

192

AN:

4826

European-Finnish (FIN)

AF:

0.234

AC:

2477

AN:

10586

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.121

AC:

8196

AN:

68002

Other (OTH)

AF:

0.110

AC:

233

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

959

1918

2876

3835

4794

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

232

464

696

928

1160

<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:

0.135

Hom.:

415

Bravo

AF:

0.144

Asia WGS

AF:

0.0480

AC:

166

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

8.1

(source)

DANN

Benign

0.68

PhyloP100

-0.46

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over