NM_001058.4:c.585-6224C>T

Variant names:

• chr2-75059979-G-A
• rs4439987
• NM_001058.4:c.585-6224C>T

Variant summary

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

The NM_001058.4(TACR1):​c.585-6224C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 152,198 control chromosomes in the GnomAD database, including 35,148 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 0.66 (35148 hom., cov: 34)
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 13 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACR1	NM_001058.4	c.585-6224C>T		intron_variant	Intron 2 of 4	ENST00000305249.10	NP_001049.1
TACR1	NM_015727.3	c.585-6224C>T		intron_variant	Intron 2 of 3		NP_056542.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACR1	ENST00000305249.10	c.585-6224C>T		intron_variant	Intron 2 of 4	1	NM_001058.4	ENSP00000303522.4
TACR1	ENST00000409848.3	c.585-6224C>T		intron_variant	Intron 2 of 3	1		ENSP00000386448.3

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100336 AN: 152080 Hom.: 35087 Cov.: 34

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.660 AC: 100460 AN: 152198 Hom.: 35148 Cov.: 34 AF XY: 0.659 AC XY: 49056 AN XY: 74406

African (AFR) AF: 0.900 AC: 37400 AN: 41552

American (AMR) AF: 0.636 AC: 9727 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1998 AN: 3472

East Asian (EAS) AF: 0.799 AC: 4144 AN: 5184

South Asian (SAS) AF: 0.671 AC: 3244 AN: 4832

European-Finnish (FIN) AF: 0.505 AC: 5342 AN: 10576

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36459 AN: 67976

Other (OTH) AF: 0.637 AC: 1346 AN: 2114

Alfa AF: 0.578 Hom.: 50712

Bravo AF: 0.678

Asia WGS AF: 0.747 AC: 2596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.59
PhyloP100		-1.1
Mutation Taster		=98/2	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: rs4439987; hg19: chr2-75287106;