2-75160927-G-C

Position:

• chr2-75160927-G-C

Variant summary

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

The NM_001058.4(TACR1):​c.389+37619C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 149,432 control chromosomes in the GnomAD database, including 23,024 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 0.55 (23024 hom., cov: 27)
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

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:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TACR1	NM_001058.4	c.389+37619C>G		intron_variant		ENST00000305249.10	NP_001049.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TACR1	ENST00000305249.10	c.389+37619C>G		intron_variant		1	NM_001058.4	ENSP00000303522.4
TACR1	ENST00000409848.3	c.389+37619C>G		intron_variant		1		ENSP00000386448.3
ENSG00000270571	ENST00000604271.2	n.318+4612G>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.552 AC: 82407 AN: 149316 Hom.: 23015 Cov.: 27

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.552 AC: 82453 AN: 149432 Hom.: 23024 Cov.: 27 AF XY: 0.555 AC XY: 40380 AN XY: 72780

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.513

Alfa AF: 0.580 Hom.: 3141

Bravo AF: 0.543

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.3
DANN	Benign	0.73

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: rs10198644; hg19: chr2-75388053;