rs10203484

Variant names:

• chr2-75174612-A-G
• rs10203484
• NM_001058.4:c.389+23934T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-75174612-A-G
• chr2-75174612-A-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+23934T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,052 control chromosomes in the GnomAD database, including 31,977 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 0.64 (31977 hom., cov: 32)
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.497
• 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 (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001058.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR1	NM_001058.4	MANE Select	c.389+23934T>C		intron	N/A	NP_001049.1
	TACR1	NM_015727.3		c.389+23934T>C		intron	N/A	NP_056542.1
	TACR1-AS1	NR_168009.1		n.372+18297A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR1	ENST00000305249.10	TSL:1 MANE Select	c.389+23934T>C		intron	N/A	ENSP00000303522.4
	TACR1	ENST00000409848.3	TSL:1	c.389+23934T>C		intron	N/A	ENSP00000386448.3
	ENSG00000270571	ENST00000604271.2	TSL:4	n.319-12218A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97636 AN: 151934 Hom.: 31944 Cov.: 32

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.643 AC: 97730 AN: 152052 Hom.: 31977 Cov.: 32 AF XY: 0.642 AC XY: 47701 AN XY: 74318

African (AFR) AF: 0.703 AC: 29176 AN: 41478

American (AMR) AF: 0.576 AC: 8805 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2245 AN: 3472

East Asian (EAS) AF: 0.338 AC: 1747 AN: 5168

South Asian (SAS) AF: 0.553 AC: 2659 AN: 4812

European-Finnish (FIN) AF: 0.699 AC: 7379 AN: 10556

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43405 AN: 67968

Other (OTH) AF: 0.616 AC: 1301 AN: 2112

Alfa AF: 0.590 Hom.: 3561

Bravo AF: 0.633

Asia WGS AF: 0.462 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.60
PhyloP100		0.50
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: rs10203484; hg19: chr2-75401738;