rs1106854

Variant names:

• chr2-75050887-T-C
• rs1106854
• NM_001058.4:c.932+364A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-75050887-T-C
• chr2-75050887-T-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+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
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001058.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR1	NM_001058.4	MANE Select	c.932+364A>G		intron	N/A	NP_001049.1
	TACR1	NM_015727.3		c.*360A>G		downstream_gene	N/A	NP_056542.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR1	ENST00000305249.10	TSL:1 MANE Select	c.932+364A>G		intron	N/A	ENSP00000303522.4
	TACR1	ENST00000409848.3	TSL:1	c.*360A>G		downstream_gene	N/A	ENSP00000386448.3

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

African (AFR) AF: 0.682 AC: 3464 AN: 5078

American (AMR) AF: 0.827 AC: 5372 AN: 6496

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 3103 AN: 4034

East Asian (EAS) AF: 0.651 AC: 4739 AN: 7276

South Asian (SAS) AF: 0.663 AC: 15625 AN: 23556

European-Finnish (FIN) AF: 0.655 AC: 4642 AN: 7090

Middle Eastern (MID) AF: 0.762 AC: 439 AN: 576

European-Non Finnish (NFE) AF: 0.703 AC: 64524 AN: 91790

Other (OTH) AF: 0.701 AC: 5709 AN: 8142

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

African (AFR) AF: 0.687 AC: 28553 AN: 41552

American (AMR) AF: 0.807 AC: 12347 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2690 AN: 3468

East Asian (EAS) AF: 0.643 AC: 3316 AN: 5160

South Asian (SAS) AF: 0.660 AC: 3181 AN: 4818

European-Finnish (FIN) AF: 0.658 AC: 6972 AN: 10598

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48341 AN: 67988

Other (OTH) AF: 0.712 AC: 1503 AN: 2112

Alfa AF: 0.626 Hom.: 1429

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
DANN	Benign	0.48
PhyloP100		-1.4
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: rs1106854; hg19: chr2-75278014;