2-75162813-G-C

Variant names:

• chr2-75162813-G-C
• rs3821319
• NM_001058.4:c.389+35733C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001058.4(TACR1):​c.389+35733C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,074 control chromosomes in the GnomAD database, including 10,807 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 0.35 (10807 hom., cov: 32)
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

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):

LOC105374811 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACR1	NM_001058.4	c.389+35733C>G		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+35733C>G		intron_variant	Intron 1 of 4	1	NM_001058.4	ENSP00000303522.4
TACR1	ENST00000409848.3	c.389+35733C>G		intron_variant	Intron 1 of 3	1		ENSP00000386448.3
ENSG00000270571	ENST00000604271.2	n.318+6498G>C		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53603 AN: 151956 Hom.: 10809 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.353 AC: 53607 AN: 152074 Hom.: 10807 Cov.: 32 AF XY: 0.361 AC XY: 26825 AN XY: 74320

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.355

Alfa AF: 0.257 Hom.: 693

Bravo AF: 0.338

Asia WGS AF: 0.406 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
DANN	Benign	0.54

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

Other links and lift over

dbSNP: rs3821319; hg19: chr2-75389939;