NM_001058.4:c.390-20903G>A

Variant names:

• chr2-75141671-C-T
• rs975664
• NM_001058.4:c.390-20903G>A

Variant summary

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

The NM_001058.4(TACR1):​c.390-20903G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 152,114 control chromosomes in the GnomAD database, including 20,247 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 0.50 (20247 hom., cov: 32)
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 9 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 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.390-20903G>A		intron	N/A	NP_001049.1	P25103-1
	TACR1	NM_015727.3		c.390-20903G>A		intron	N/A	NP_056542.1	P25103-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR1	ENST00000305249.10	TSL:1 MANE Select	c.390-20903G>A		intron	N/A	ENSP00000303522.4	P25103-1
	TACR1	ENST00000409848.3	TSL:1	c.390-20903G>A		intron	N/A	ENSP00000386448.3	P25103-3

Frequencies

GnomAD3 genomes AF: 0.500 AC: 76039 AN: 151996 Hom.: 20235 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.0249

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.500 AC: 76090 AN: 152114 Hom.: 20247 Cov.: 32 AF XY: 0.489 AC XY: 36388 AN XY: 74372

African (AFR) AF: 0.596 AC: 24722 AN: 41492

American (AMR) AF: 0.407 AC: 6218 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1560 AN: 3470

East Asian (EAS) AF: 0.0245 AC: 127 AN: 5178

South Asian (SAS) AF: 0.283 AC: 1366 AN: 4822

European-Finnish (FIN) AF: 0.461 AC: 4875 AN: 10570

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35596 AN: 67978

Other (OTH) AF: 0.465 AC: 984 AN: 2114

Alfa AF: 0.509 Hom.: 57803

Bravo AF: 0.498

Asia WGS AF: 0.214 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.14
DANN	Benign	0.47
PhyloP100		-1.5
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: rs975664; hg19: chr2-75368797;