Variant 4-103719946-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001059.3(TACR3):c.-271C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 555,554 control chromosomes in the GnomAD database, including 25,544 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.34 ( 13257 hom., cov: 32)

Exomes 𝑓: 0.22 ( 12287 hom. )

Consequence

TACR3
NM_001059.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.932

Variant links:

Genes affected

TACR3 (HGNC:11528): (tachykinin receptor 3) This gene belongs to a family of genes that function as receptors for tachykinins. Receptor affinities are specified by variations in the 5'-end of the sequence. The receptors belonging to this family are characterized by interactions with G proteins and 7 hydrophobic transmembrane regions. This gene encodes the receptor for the tachykinin neurokinin 3, also referred to as neurokinin B. [provided by RefSeq, Jul 2008]

TACR3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 4-103719946-G-C is Benign according to our data. Variant chr4-103719946-G-C is described in ClinVar as [Benign]. Clinvar id is 672984.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TACR3	NM_001059.3 link	c.-271C>G		5_prime_UTR_variant	1/5	ENST00000304883.3	NP_001050.1	P29371

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TACR3	ENST00000304883.3 link	c.-271C>G		5_prime_UTR_variant	1/5	1	NM_001059.3	ENSP00000303325.2		P29371

Frequencies

GnomAD3 genomes

AF:

0.337

AC:

51128

AN:

151884

Hom.:

13215

Cov.:

show subpopulations

Gnomad AFR

AF:

0.725

Gnomad AMI

AF:

0.204

Gnomad AMR

AF:

0.244

Gnomad ASJ

AF:

0.173

Gnomad EAS

AF:

0.361

Gnomad SAS

AF:

0.334

Gnomad FIN

AF:

0.177

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.307

GnomAD4 exome

AF:

0.217

AC:

87478

AN:

403552

Hom.:

12287

AF XY:

0.221

AC XY:

46491

AN XY:

210590

show subpopulations

Gnomad4 AFR exome

AF:

0.733

Gnomad4 AMR exome

AF:

0.226

Gnomad4 ASJ exome

AF:

0.186

Gnomad4 EAS exome

AF:

0.365

Gnomad4 SAS exome

AF:

0.335

Gnomad4 FIN exome

AF:

0.167

Gnomad4 NFE exome

AF:

0.160

Gnomad4 OTH exome

AF:

0.229

GnomAD4 genome

AF:

0.337

AC:

51227

AN:

152002

Hom.:

13257

Cov.:

AF XY:

0.336

AC XY:

24997

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.726

Gnomad4 AMR

AF:

0.244

Gnomad4 ASJ

AF:

0.173

Gnomad4 EAS

AF:

0.361

Gnomad4 SAS

AF:

0.333

Gnomad4 FIN

AF:

0.177

Gnomad4 NFE

AF:

0.156

Gnomad4 OTH

AF:

0.307

Alfa

AF:

0.116

Hom.:

271

Bravo

AF:

0.356

Asia WGS

AF:

0.369

AC:

1286

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.1

DANN

Benign

0.30

Splicing

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over