Genetic Variant TACR1:c.932+364A>C (chr2-75050887-T-G) – 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.932+364A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0474 in 306,672 control chromosomes in the GnomAD database, including 671 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 0.060 ( 491 hom., cov: 33)

Exomes 𝑓: 0.035 ( 180 hom. )

Consequence

TACR1
NM_001058.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.44

Publications

3 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACR1	NM_001058.4 link	c.932+364A>C		intron_variant	Intron 4 of 4	ENST00000305249.10	NP_001049.1	P25103-1
TACR1	NM_015727.3 link	c.*360A>C		downstream_gene_variant			NP_056542.1	P25103-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACR1	ENST00000305249.10 link	c.932+364A>C		intron_variant	Intron 4 of 4	1	NM_001058.4	ENSP00000303522.4		P25103-1
TACR1	ENST00000409848.3 link	c.*360A>C		downstream_gene_variant		1		ENSP00000386448.3		P25103-3

Frequencies

GnomAD3 genomes

AF:

0.0596

AC:

9073

AN:

152110

Hom.:

493

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.0378

Gnomad ASJ

AF:

0.0395

Gnomad EAS

AF:

0.00502

Gnomad SAS

AF:

0.0800

Gnomad FIN

AF:

0.0173

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0231

Gnomad OTH

AF:

0.0603

GnomAD4 exome

AF:

0.0353

AC:

5456

AN:

154444

Hom.:

180

AF XY:

0.0380

AC XY:

3107

AN XY:

81744

show subpopulations

African (AFR)

AF:

0.147

AC:

748

AN:

5076

American (AMR)

AF:

0.0305

AC:

198

AN:

6500

Ashkenazi Jewish (ASJ)

AF:

0.0400

AC:

162

AN:

4048

East Asian (EAS)

AF:

0.00288

AC:

AN:

7298

South Asian (SAS)

AF:

0.0740

AC:

1746

AN:

23608

European-Finnish (FIN)

AF:

0.0191

AC:

136

AN:

7116

Middle Eastern (MID)

AF:

0.0677

AC:

AN:

576

European-Non Finnish (NFE)

AF:

0.0232

AC:

2133

AN:

92052

Other (OTH)

AF:

0.0334

AC:

273

AN:

8170

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

244

488

733

977

1221

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

104

156

208

260

<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:

0.0597

AC:

9087

AN:

152228

Hom.:

491

Cov.:

AF XY:

0.0587

AC XY:

4373

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.146

AC:

6058

AN:

41562

American (AMR)

AF:

0.0378

AC:

578

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0395

AC:

137

AN:

3468

East Asian (EAS)

AF:

0.00503

AC:

AN:

5166

South Asian (SAS)

AF:

0.0798

AC:

385

AN:

4822

European-Finnish (FIN)

AF:

0.0173

AC:

183

AN:

10604

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0231

AC:

1571

AN:

67992

Other (OTH)

AF:

0.0616

AC:

130

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

405

809

1214

1618

2023

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

294

392

490

<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:

0.0175

Hom.:

1429

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.37

(source)

DANN

Benign

0.53

PhyloP100

-1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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