rs12713828

Variant names:

• chr2-75048954-G-A
• rs12713828
• NM_001058.4:c.*478C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001058.4(TACR1):​c.*478C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 155,870 control chromosomes in the GnomAD database, including 12,490 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 0.39 (12181 hom., cov: 32)
  • Exomes 𝑓: 0.37 (309 hom.)
• Consequence: TACR1 NM_001058.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151
• Publications: 15 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACR1	NM_001058.4	c.*478C>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000305249.10	NP_001049.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACR1	ENST00000305249.10	c.*478C>T		3_prime_UTR_variant	Exon 5 of 5	1	NM_001058.4	ENSP00000303522.4

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59836 AN: 151976 Hom.: 12181 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.427

GnomAD4 exome AF: 0.375 AC: 1415 AN: 3778 Hom.: 309 Cov.: 0 AF XY: 0.373 AC XY: 708 AN XY: 1898

African (AFR) AF: 0.273 AC: 18 AN: 66

American (AMR) AF: 0.298 AC: 181 AN: 608

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 32 AN: 72

East Asian (EAS) AF: 0.349 AC: 30 AN: 86

South Asian (SAS) AF: 0.286 AC: 40 AN: 140

European-Finnish (FIN) AF: 0.268 AC: 22 AN: 82

Middle Eastern (MID) AF: 0.250 AC: 1 AN: 4

European-Non Finnish (NFE) AF: 0.404 AC: 1032 AN: 2556

Other (OTH) AF: 0.360 AC: 59 AN: 164

GnomAD4 genome AF: 0.394 AC: 59854 AN: 152092 Hom.: 12181 Cov.: 32 AF XY: 0.388 AC XY: 28845 AN XY: 74368

African (AFR) AF: 0.320 AC: 13256 AN: 41486

American (AMR) AF: 0.405 AC: 6194 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1988 AN: 3470

East Asian (EAS) AF: 0.434 AC: 2243 AN: 5170

South Asian (SAS) AF: 0.309 AC: 1486 AN: 4814

European-Finnish (FIN) AF: 0.313 AC: 3310 AN: 10572

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29887 AN: 67980

Other (OTH) AF: 0.422 AC: 890 AN: 2108

Alfa AF: 0.423 Hom.: 21326

Bravo AF: 0.400

Asia WGS AF: 0.355 AC: 1235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.46
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12713828; hg19: chr2-75276081;