chr2-75188610-T-G

Position:

• chr2-75188610-T-G

Variant summary

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

The NM_001058.4(TACR1):​c.389+9936A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,004 control chromosomes in the GnomAD database, including 3,512 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 0.21 (3511 hom., cov: 32)
  • Exomes 𝑓: 0.15 (1 hom.)
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TACR1	NM_001058.4	c.389+9936A>C		intron_variant		ENST00000305249.10
LOC105374811	NR_168009.1	n.372+32295T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TACR1	ENST00000305249.10	c.389+9936A>C		intron_variant		1	NM_001058.4	P1
TACR1	ENST00000409848.3	c.389+9936A>C		intron_variant		1
	ENST00000604271.2	n.2099T>G		non_coding_transcript_exon_variant	3/3	4

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31915 AN: 151866 Hom.: 3513 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0728

Gnomad SAS AF: 0.0937

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.227

GnomAD4 exome AF: 0.150 AC: 3 AN: 20 Hom.: 1 Cov.: 0 AF XY: 0.0625 AC XY: 1 AN XY: 16

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.125

GnomAD4 genome AF: 0.210 AC: 31912 AN: 151984 Hom.: 3511 Cov.: 32 AF XY: 0.207 AC XY: 15353 AN XY: 74294

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.0731

Gnomad4 SAS AF: 0.0934

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.226

Alfa AF: 0.225 Hom.: 657

Bravo AF: 0.214

Asia WGS AF: 0.116 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.76
DANN	Benign	0.48

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: rs3771860; hg19: chr2-75415736;