rs726506

Variant names:

• chr2-75181892-C-G
• rs726506
• NM_001058.4:c.389+16654G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-75181892-C-G
• chr2-75181892-C-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.389+16654G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,050 control chromosomes in the GnomAD database, including 15,292 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 (15292 hom., cov: 32)
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 5 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]

ENSG00000270571 (HGNC:58209):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACR1	NM_001058.4	c.389+16654G>C		intron_variant	Intron 1 of 4	ENST00000305249.10	NP_001049.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACR1	ENST00000305249.10	c.389+16654G>C		intron_variant	Intron 1 of 4	1	NM_001058.4	ENSP00000303522.4
TACR1	ENST00000409848.3	c.389+16654G>C		intron_variant	Intron 1 of 3	1		ENSP00000386448.3
ENSG00000270571	ENST00000604271.2	n.319-4938C>G		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64934 AN: 151932 Hom.: 15294 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.427

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.427 AC: 64961 AN: 152050 Hom.: 15292 Cov.: 32 AF XY: 0.434 AC XY: 32219 AN XY: 74280

African (AFR) AF: 0.243 AC: 10084 AN: 41484

American (AMR) AF: 0.446 AC: 6821 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1563 AN: 3470

East Asian (EAS) AF: 0.294 AC: 1525 AN: 5180

South Asian (SAS) AF: 0.490 AC: 2353 AN: 4806

European-Finnish (FIN) AF: 0.569 AC: 6003 AN: 10556

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34843 AN: 67958

Other (OTH) AF: 0.425 AC: 898 AN: 2112

Alfa AF: 0.471 Hom.: 2220

Bravo AF: 0.406

Asia WGS AF: 0.365 AC: 1270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.064
DANN	Benign	0.55
PhyloP100		-1.8
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: rs726506; hg19: chr2-75409018;