chr2-75160927-G-C

Variant names:

• chr2-75160927-G-C
• rs10198644
• NM_001058.4:c.389+37619C>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.389+37619C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 149,432 control chromosomes in the GnomAD database, including 23,024 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 0.55 (23024 hom., cov: 27)
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• 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]

TACR1-AS1 (HGNC:58209):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 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.389+37619C>G		intron	N/A	NP_001049.1	P25103-1
	TACR1	NM_015727.3		c.389+37619C>G		intron	N/A	NP_056542.1	P25103-3
	TACR1-AS1	NR_168009.1		n.372+4612G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR1	ENST00000305249.10	TSL:1 MANE Select	c.389+37619C>G		intron	N/A	ENSP00000303522.4	P25103-1
	TACR1	ENST00000409848.3	TSL:1	c.389+37619C>G		intron	N/A	ENSP00000386448.3	P25103-3
	TACR1-AS1	ENST00000604271.2	TSL:4	n.318+4612G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.552 AC: 82407 AN: 149316 Hom.: 23015 Cov.: 27

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.552 AC: 82453 AN: 149432 Hom.: 23024 Cov.: 27 AF XY: 0.555 AC XY: 40380 AN XY: 72780

African (AFR) AF: 0.514 AC: 20987 AN: 40806

American (AMR) AF: 0.550 AC: 8196 AN: 14912

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1962 AN: 3432

East Asian (EAS) AF: 0.451 AC: 2277 AN: 5050

South Asian (SAS) AF: 0.554 AC: 2593 AN: 4678

European-Finnish (FIN) AF: 0.647 AC: 6494 AN: 10040

Middle Eastern (MID) AF: 0.476 AC: 136 AN: 286

European-Non Finnish (NFE) AF: 0.568 AC: 38204 AN: 67244

Other (OTH) AF: 0.513 AC: 1070 AN: 2086

Alfa AF: 0.580 Hom.: 3141

Bravo AF: 0.543

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.3
DANN	Benign	0.73
PhyloP100		0.21
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: rs10198644; hg19: chr2-75388053;