rs3771825

Variant names:

• chr2-75128354-C-T
• rs3771825
• NM_001058.4:c.390-7586G>A

Variant summary

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

The NM_001058.4(TACR1):​c.390-7586G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,134 control chromosomes in the GnomAD database, including 4,749 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 0.21 (4749 hom., cov: 33)
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACR1	NM_001058.4	c.390-7586G>A		intron_variant	Intron 1 of 4	ENST00000305249.10	NP_001049.1
TACR1	NM_015727.3	c.390-7586G>A		intron_variant	Intron 1 of 3		NP_056542.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACR1	ENST00000305249.10	c.390-7586G>A		intron_variant	Intron 1 of 4	1	NM_001058.4	ENSP00000303522.4
TACR1	ENST00000409848.3	c.390-7586G>A		intron_variant	Intron 1 of 3	1		ENSP00000386448.3

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32027 AN: 152016 Hom.: 4744 Cov.: 33

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.0583

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.211 AC: 32065 AN: 152134 Hom.: 4749 Cov.: 33 AF XY: 0.212 AC XY: 15758 AN XY: 74382

African (AFR) AF: 0.372 AC: 15411 AN: 41482

American (AMR) AF: 0.271 AC: 4140 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2303 AN: 5162

South Asian (SAS) AF: 0.263 AC: 1266 AN: 4812

European-Finnish (FIN) AF: 0.0583 AC: 619 AN: 10610

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7002 AN: 68000

Other (OTH) AF: 0.202 AC: 426 AN: 2110

Alfa AF: 0.136 Hom.: 1140

Bravo AF: 0.238

Asia WGS AF: 0.322 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.74
DANN	Benign	0.72
PhyloP100		0.095
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: rs3771825; hg19: chr2-75355480;