2-75162813-G-C

Variant names:

• chr2-75162813-G-C
• rs3821319
• NM_001058.4:c.389+35733C>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+35733C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,074 control chromosomes in the GnomAD database, including 10,807 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 0.35 (10807 hom., cov: 32)
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 2 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=-0.56).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 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+35733C>G		intron	N/A	NP_001049.1	P25103-1
	TACR1	NM_015727.3		c.389+35733C>G		intron	N/A	NP_056542.1	P25103-3
	TACR1-AS1	NR_168009.1		n.372+6498G>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+35733C>G		intron	N/A	ENSP00000303522.4	P25103-1
	TACR1	ENST00000409848.3	TSL:1	c.389+35733C>G		intron	N/A	ENSP00000386448.3	P25103-3
	TACR1-AS1	ENST00000604271.2	TSL:4	n.318+6498G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53603 AN: 151956 Hom.: 10809 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.353 AC: 53607 AN: 152074 Hom.: 10807 Cov.: 32 AF XY: 0.361 AC XY: 26825 AN XY: 74320

African (AFR) AF: 0.134 AC: 5564 AN: 41474

American (AMR) AF: 0.454 AC: 6945 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1595 AN: 3472

East Asian (EAS) AF: 0.373 AC: 1927 AN: 5172

South Asian (SAS) AF: 0.503 AC: 2429 AN: 4830

European-Finnish (FIN) AF: 0.467 AC: 4935 AN: 10562

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28854 AN: 67952

Other (OTH) AF: 0.355 AC: 750 AN: 2112

Alfa AF: 0.257 Hom.: 693

Bravo AF: 0.338

Asia WGS AF: 0.406 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
DANN	Benign	0.54
PhyloP100		1.2
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: rs3821319; hg19: chr2-75389939;