rs1384401

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000304883.3(TACR3):​c.888+12273C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,492 control chromosomes in the GnomAD database, including 17,211 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 0.43 ( 17211 hom., cov: 32)

Consequence

TACR3
ENST00000304883.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0300
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TACR3NM_001059.3 linkuse as main transcriptc.888+12273C>T intron_variant ENST00000304883.3 NP_001050.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TACR3ENST00000304883.3 linkuse as main transcriptc.888+12273C>T intron_variant 1 NM_001059.3 ENSP00000303325 P1

Frequencies

GnomAD3 genomes
AF:
0.434
AC:
65707
AN:
151376
Hom.:
17168
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.746
Gnomad AMI
AF:
0.408
Gnomad AMR
AF:
0.333
Gnomad ASJ
AF:
0.310
Gnomad EAS
AF:
0.257
Gnomad SAS
AF:
0.299
Gnomad FIN
AF:
0.245
Gnomad MID
AF:
0.354
Gnomad NFE
AF:
0.327
Gnomad OTH
AF:
0.415
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.434
AC:
65803
AN:
151492
Hom.:
17211
Cov.:
32
AF XY:
0.426
AC XY:
31515
AN XY:
74036
show subpopulations
Gnomad4 AFR
AF:
0.746
Gnomad4 AMR
AF:
0.332
Gnomad4 ASJ
AF:
0.310
Gnomad4 EAS
AF:
0.257
Gnomad4 SAS
AF:
0.299
Gnomad4 FIN
AF:
0.245
Gnomad4 NFE
AF:
0.327
Gnomad4 OTH
AF:
0.415
Alfa
AF:
0.379
Hom.:
2603
Bravo
AF:
0.452
Asia WGS
AF:
0.314
AC:
1092
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
1.3
DANN
Benign
0.30

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.

Other links and lift over

dbSNP: rs1384401; hg19: chr4-104565078; API