rs1106854

chr2-75050887-T-Cchr2-75050887-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.932+364A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 306,232 control chromosomes in the GnomAD database, including 76,479 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 0.71 (38399 hom., cov: 33)
  • Exomes 𝑓: 0.70 (38080 hom.)
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TACR1	NM_001058.4	c.932+364A>G		intron_variant		ENST00000305249.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TACR1	ENST00000305249.10	c.932+364A>G		intron_variant		1	NM_001058.4	P1

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107788 AN: 152076 Hom.: 38362 Cov.: 33

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.716

GnomAD4 exome AF: 0.699 AC: 107617 AN: 154038 Hom.: 38080 AF XY: 0.695 AC XY: 56680 AN XY: 81546

Gnomad4 AFR exome AF: 0.682

Gnomad4 AMR exome AF: 0.827

Gnomad4 ASJ exome AF: 0.769

Gnomad4 EAS exome AF: 0.651

Gnomad4 SAS exome AF: 0.663

Gnomad4 FIN exome AF: 0.655

Gnomad4 NFE exome AF: 0.703

Gnomad4 OTH exome AF: 0.701

GnomAD4 genome AF: 0.709 AC: 107883 AN: 152194 Hom.: 38399 Cov.: 33 AF XY: 0.708 AC XY: 52719 AN XY: 74412

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.712

Alfa AF: 0.602 Hom.: 1179

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.35
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: rs1106854; hg19: chr2-75278014;