Genetic Variant NM_001058.4:c.389+9936A>C (chr2-75188610-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.389+9936A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,004 control chromosomes in the GnomAD database, including 3,512 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 0.21 ( 3511 hom., cov: 32)

Exomes 𝑓: 0.15 ( 1 hom. )

Consequence

TACR1
NM_001058.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.340

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:

ENSG00000270571 (HGNC:58209):

ENSG00000270571 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=-0.97).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACR1	NM_001058.4 link	c.389+9936A>C		intron_variant	Intron 1 of 4	ENST00000305249.10	NP_001049.1	P25103-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TACR1	ENST00000305249.10 link	c.389+9936A>C	intron_variant	Intron 1 of 4	1	NM_001058.4	ENSP00000303522.4	P25103-1
TACR1	ENST00000409848.3 link	c.389+9936A>C	intron_variant	Intron 1 of 3	1		ENSP00000386448.3	P25103-3
ENSG00000270571	ENST00000604271.2 link	n.2099T>G	non_coding_transcript_exon_variant	Exon 3 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.210

AC:

31915

AN:

151866

Hom.:

3513

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.152

Gnomad AMR

AF:

0.249

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.0728

Gnomad SAS

AF:

0.0937

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.227

GnomAD4 exome

AF:

0.150

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0625

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.125

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.210

AC:

31912

AN:

151984

Hom.:

3511

Cov.:

AF XY:

0.207

AC XY:

15353

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.180

AC:

7442

AN:

41448

American (AMR)

AF:

0.248

AC:

3793

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.199

AC:

689

AN:

3468

East Asian (EAS)

AF:

0.0731

AC:

378

AN:

5168

South Asian (SAS)

AF:

0.0934

AC:

450

AN:

4818

European-Finnish (FIN)

AF:

0.207

AC:

2186

AN:

10554

Middle Eastern (MID)

AF:

0.245

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.240

AC:

16287

AN:

67942

Other (OTH)

AF:

0.226

AC:

477

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1296

2591

3887

5182

6478

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

334

668

1002

1336

1670

<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:

0.225

Hom.:

657

Bravo

AF:

0.214

Asia WGS

AF:

0.116

AC:

404

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.76

(source)

DANN

Benign

0.48

PhyloP100

-0.34

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over