2-75188293-T-C

Position:

• chr2-75188293-T-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+10253A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 152,150 control chromosomes in the GnomAD database, including 11,559 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 0.38 (11559 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TACR1	NM_001058.4	c.389+10253A>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+10253A>G		intron_variant		1	NM_001058.4	ENSP00000303522.4
TACR1	ENST00000409848.3	c.389+10253A>G		intron_variant		1		ENSP00000386448.3
ENSG00000270571	ENST00000604271.2	n.1782T>C		non_coding_transcript_exon_variant	3/3	4

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57796 AN: 152032 Hom.: 11556 Cov.: 33

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.385

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.380 AC: 57839 AN: 152150 Hom.: 11559 Cov.: 33 AF XY: 0.380 AC XY: 28289 AN XY: 74380

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.383

Alfa AF: 0.332 Hom.: 10079

Bravo AF: 0.395

Asia WGS AF: 0.387 AC: 1342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.8
DANN	Benign	0.72

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: rs2193409; hg19: chr2-75415419;