rs11126453

chr2-75141614-C-T

Variant summary

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

The NM_001058.4(TACR1):c.390-20846G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 151,972 control chromosomes in the GnomAD database, including 1,284 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 0.12 (1284 hom., cov: 32)
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TACR1	NM_001058.4	c.390-20846G>A		intron_variant		ENST00000305249.10
TACR1	NM_015727.3	c.390-20846G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TACR1	ENST00000305249.10	c.390-20846G>A		intron_variant		1	NM_001058.4	P1
TACR1	ENST00000409848.3	c.390-20846G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18282 AN: 151874 Hom.: 1285 Cov.: 32

Gnomad AFR AF: 0.0953

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.120 AC: 18295 AN: 151972 Hom.: 1284 Cov.: 32 AF XY: 0.122 AC XY: 9081 AN XY: 74268

Gnomad4 AFR AF: 0.0953

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.0713

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.145

Alfa AF: 0.123 Hom.: 1131

Bravo AF: 0.134

Asia WGS AF: 0.180 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.4
Dann	Benign	0.31

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: rs11126453; hg19: chr2-75368740;