2-75139811-C-T

Position:

• chr2-75139811-C-T

Variant summary

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

The ENST00000305249.10(TACR1):​c.390-19043G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,060 control chromosomes in the GnomAD database, including 1,644 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 0.14 (1644 hom., cov: 32)
• Consequence: TACR1 ENST00000305249.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.641

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=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TACR1	NM_001058.4	c.390-19043G>A		intron_variant		ENST00000305249.10	NP_001049.1
TACR1	NM_015727.3	c.390-19043G>A		intron_variant			NP_056542.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TACR1	ENST00000305249.10	c.390-19043G>A		intron_variant		1	NM_001058.4	ENSP00000303522	P1
TACR1	ENST00000409848.3	c.390-19043G>A		intron_variant		1		ENSP00000386448

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21359 AN: 151942 Hom.: 1646 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.141 AC: 21375 AN: 152060 Hom.: 1644 Cov.: 32 AF XY: 0.142 AC XY: 10561 AN XY: 74322

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.159

Alfa AF: 0.128 Hom.: 2774

Bravo AF: 0.154

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	14
DANN	Benign	0.68

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: rs3771833; hg19: chr2-75366937;