2-75050860-T-C

Variant names:

• chr2-75050860-T-C
• rs1106855
• NM_001058.4:c.932+391A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001058.4(TACR1):​c.932+391A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,232 control chromosomes in the GnomAD database, including 45,249 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 0.77 (45249 hom., cov: 33)
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACR1	NM_001058.4	c.932+391A>G		intron_variant	Intron 4 of 4	ENST00000305249.10	NP_001049.1
TACR1	NM_015727.3	c.*387A>G		downstream_gene_variant			NP_056542.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACR1	ENST00000305249.10	c.932+391A>G		intron_variant	Intron 4 of 4	1	NM_001058.4	ENSP00000303522.4
TACR1	ENST00000409848.3	c.*387A>G		downstream_gene_variant		1		ENSP00000386448.3

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116831 AN: 152114 Hom.: 45196 Cov.: 33

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.768 AC: 116940 AN: 152232 Hom.: 45249 Cov.: 33 AF XY: 0.767 AC XY: 57079 AN XY: 74428

African (AFR) AF: 0.831 AC: 34552 AN: 41564

American (AMR) AF: 0.845 AC: 12931 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2828 AN: 3470

East Asian (EAS) AF: 0.648 AC: 3351 AN: 5170

South Asian (SAS) AF: 0.741 AC: 3575 AN: 4824

European-Finnish (FIN) AF: 0.675 AC: 7155 AN: 10596

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49919 AN: 67990

Other (OTH) AF: 0.773 AC: 1630 AN: 2110

Alfa AF: 0.755 Hom.: 15415

Bravo AF: 0.784

Asia WGS AF: 0.701 AC: 2440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.23
DANN	Benign	0.43
PhyloP100		-0.93
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1106855; hg19: chr2-75277987;