rs3771810

chr2-75080526-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.585-26771A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,078 control chromosomes in the GnomAD database, including 4,310 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 0.22 (4310 hom., cov: 32)
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.31

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TACR1	NM_001058.4	c.585-26771A>G		intron_variant		ENST00000305249.10
TACR1	NM_015727.3	c.585-26771A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TACR1	ENST00000305249.10	c.585-26771A>G		intron_variant		1	NM_001058.4	P1
TACR1	ENST00000409848.3	c.585-26771A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32902 AN: 151958 Hom.: 4286 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.217 AC: 32979 AN: 152078 Hom.: 4310 Cov.: 32 AF XY: 0.219 AC XY: 16250 AN XY: 74346

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.0971

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.215

Alfa AF: 0.211 Hom.: 868

Bravo AF: 0.240

Asia WGS AF: 0.290 AC: 1006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.047
Dann	Benign	0.71

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: rs3771810; hg19: chr2-75307653;