rs3771856

Positions:

• chr2-75186888-G-A

Variant summary

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

The ENST00000305249.10(TACR1):​c.389+11658C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 152,118 control chromosomes in the GnomAD database, including 26,355 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 0.56 (26355 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: TACR1 ENST00000305249.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TACR1	NM_001058.4	c.389+11658C>T		intron_variant		ENST00000305249.10	NP_001049.1
LOC105374811	NR_168009.1	n.372+30573G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TACR1	ENST00000305249.10	c.389+11658C>T		intron_variant		1	NM_001058.4	ENSP00000303522	P1
TACR1	ENST00000409848.3	c.389+11658C>T		intron_variant		1		ENSP00000386448
	ENST00000604271.2	n.377G>A		non_coding_transcript_exon_variant	3/3	4

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85179 AN: 151998 Hom.: 26319 Cov.: 33

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.529

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.561 AC: 85276 AN: 152116 Hom.: 26355 Cov.: 33 AF XY: 0.554 AC XY: 41171 AN XY: 74340

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.527

Alfa AF: 0.521 Hom.: 2745

Bravo AF: 0.580

Asia WGS AF: 0.449 AC: 1560 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	3.4
DANN	Benign	0.41

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: rs3771856; hg19: chr2-75414014;