Variant rs6715729 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001058.4(TACR1):c.333T>C(p.Phe111=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 1,613,960 control chromosomes in the GnomAD database, including 198,090 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 0.57 ( 27179 hom., cov: 33)

Exomes 𝑓: 0.48 ( 170911 hom. )

Consequence

TACR1
NM_001058.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.12

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:

LOC105374811 (HGNC:):

LOC105374811 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP7

Synonymous conserved (PhyloP=2.12 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
TACR1	NM_001058.4 linkuse as main transcript	c.333T>C	p.Phe111=	synonymous_variant	1/5	ENST00000305249.10	NP_001049.1
LOC105374811	NR_168009.1 linkuse as main transcript	n.372+42287A>G		intron_variant, non_coding_transcript_variant
TACR1	NM_015727.3 linkuse as main transcript	c.333T>C	p.Phe111=	synonymous_variant	1/4		NP_056542.1
LOC105374811	NR_168010.1 linkuse as main transcript	n.366+42287A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TACR1	ENST00000305249.10 linkuse as main transcript	c.333T>C	p.Phe111=	synonymous_variant	1/5	1	NM_001058.4	ENSP00000303522	P1	P25103-1
TACR1	ENST00000409848.3 linkuse as main transcript	c.333T>C	p.Phe111=	synonymous_variant	1/4	1		ENSP00000386448		P25103-3

Frequencies

GnomAD3 genomes

AF:

0.571

AC:

86736

AN:

152010

Hom.:

27143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.852

Gnomad AMI

AF:

0.288

Gnomad AMR

AF:

0.493

Gnomad ASJ

AF:

0.378

Gnomad EAS

AF:

0.404

Gnomad SAS

AF:

0.405

Gnomad FIN

AF:

0.438

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.476

Gnomad OTH

AF:

0.543

GnomAD3 exomes

AF:

0.476

AC:

119661

AN:

251454

Hom.:

29933

AF XY:

0.465

AC XY:

63205

AN XY:

135896

show subpopulations

Gnomad AFR exome

AF:

0.861

Gnomad AMR exome

AF:

0.456

Gnomad ASJ exome

AF:

0.378

Gnomad EAS exome

AF:

0.407

Gnomad SAS exome

AF:

0.400

Gnomad FIN exome

AF:

0.435

Gnomad NFE exome

AF:

0.475

Gnomad OTH exome

AF:

0.461

GnomAD4 exome

AF:

0.478

AC:

699391

AN:

1461832

Hom.:

170911

Cov.:

AF XY:

0.474

AC XY:

344648

AN XY:

727214

show subpopulations

Gnomad4 AFR exome

AF:

0.868

Gnomad4 AMR exome

AF:

0.462

Gnomad4 ASJ exome

AF:

0.382

Gnomad4 EAS exome

AF:

0.439

Gnomad4 SAS exome

AF:

0.396

Gnomad4 FIN exome

AF:

0.432

Gnomad4 NFE exome

AF:

0.480

Gnomad4 OTH exome

AF:

0.480

GnomAD4 genome

AF:

0.571

AC:

86833

AN:

152128

Hom.:

27179

Cov.:

AF XY:

0.563

AC XY:

41870

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.852

Gnomad4 AMR

AF:

0.492

Gnomad4 ASJ

AF:

0.378

Gnomad4 EAS

AF:

0.404

Gnomad4 SAS

AF:

0.406

Gnomad4 FIN

AF:

0.438

Gnomad4 NFE

AF:

0.476

Gnomad4 OTH

AF:

0.540

Alfa

AF:

0.515

Hom.:

10150

Bravo

AF:

0.590

Asia WGS

AF:

0.449

AC:

1560

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.73

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over