Genetic Variant NM_001058.4:c.932+364A>G (chr2-75050887-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.932+364A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 306,232 control chromosomes in the GnomAD database, including 76,479 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 0.71 ( 38399 hom., cov: 33)

Exomes 𝑓: 0.70 ( 38080 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=-0.99).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.795 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>G		intron_variant	Intron 4 of 4	ENST00000305249.10	NP_001049.1	P25103-1
TACR1	NM_015727.3 link	c.*360A>G		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>G		intron_variant	Intron 4 of 4	1	NM_001058.4	ENSP00000303522.4		P25103-1
TACR1	ENST00000409848.3 link	c.*360A>G		downstream_gene_variant		1		ENSP00000386448.3		P25103-3

Frequencies

GnomAD3 genomes

AF:

0.709

AC:

107788

AN:

152076

Hom.:

38362

Cov.:

show subpopulations

Gnomad AFR

AF:

0.687

Gnomad AMI

AF:

0.809

Gnomad AMR

AF:

0.807

Gnomad ASJ

AF:

0.776

Gnomad EAS

AF:

0.643

Gnomad SAS

AF:

0.660

Gnomad FIN

AF:

0.658

Gnomad MID

AF:

0.810

Gnomad NFE

AF:

0.711

Gnomad OTH

AF:

0.716

GnomAD4 exome

AF:

0.699

AC:

107617

AN:

154038

Hom.:

38080

AF XY:

0.695

AC XY:

56680

AN XY:

81546

show subpopulations

African (AFR)

AF:

0.682

AC:

3464

AN:

5078

American (AMR)

AF:

0.827

AC:

5372

AN:

6496

Ashkenazi Jewish (ASJ)

AF:

0.769

AC:

3103

AN:

4034

East Asian (EAS)

AF:

0.651

AC:

4739

AN:

7276

South Asian (SAS)

AF:

0.663

AC:

15625

AN:

23556

European-Finnish (FIN)

AF:

0.655

AC:

4642

AN:

7090

Middle Eastern (MID)

AF:

0.762

AC:

439

AN:

576

European-Non Finnish (NFE)

AF:

0.703

AC:

64524

AN:

91790

Other (OTH)

AF:

0.701

AC:

5709

AN:

8142

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1507

3014

4520

6027

7534

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

424

848

1272

1696

2120

<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:

0.709

AC:

107883

AN:

152194

Hom.:

38399

Cov.:

AF XY:

0.708

AC XY:

52719

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.687

AC:

28553

AN:

41552

American (AMR)

AF:

0.807

AC:

12347

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.776

AC:

2690

AN:

3468

East Asian (EAS)

AF:

0.643

AC:

3316

AN:

5160

South Asian (SAS)

AF:

0.660

AC:

3181

AN:

4818

European-Finnish (FIN)

AF:

0.658

AC:

6972

AN:

10598

Middle Eastern (MID)

AF:

0.823

AC:

242

AN:

294

European-Non Finnish (NFE)

AF:

0.711

AC:

48341

AN:

67988

Other (OTH)

AF:

0.712

AC:

1503

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1589

3178

4766

6355

7944

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

836

1672

2508

3344

4180

<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:

0.626

Hom.:

1429

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.35

(source)

DANN

Benign

0.48

PhyloP100

-1.4

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over