rs3771863

Variant names:

• chr2-75192588-C-T
• rs3771863
• NM_001058.4:c.389+5958G>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.389+5958G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,030 control chromosomes in the GnomAD database, including 9,618 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 0.30 (9618 hom., cov: 32)
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.11
• Publications: 17 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR1	NM_001058.4	MANE Select	c.389+5958G>A		intron	N/A	NP_001049.1
	TACR1	NM_015727.3		c.389+5958G>A		intron	N/A	NP_056542.1
	TACR1-AS1	NR_168009.1		n.372+36273C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR1	ENST00000305249.10	TSL:1 MANE Select	c.389+5958G>A		intron	N/A	ENSP00000303522.4
	TACR1	ENST00000409848.3	TSL:1	c.389+5958G>A		intron	N/A	ENSP00000386448.3

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45632 AN: 151912 Hom.: 9590 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.301 AC: 45710 AN: 152030 Hom.: 9618 Cov.: 32 AF XY: 0.298 AC XY: 22153 AN XY: 74320

African (AFR) AF: 0.604 AC: 24976 AN: 41374

American (AMR) AF: 0.206 AC: 3155 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3468

East Asian (EAS) AF: 0.319 AC: 1650 AN: 5168

South Asian (SAS) AF: 0.295 AC: 1419 AN: 4818

European-Finnish (FIN) AF: 0.156 AC: 1653 AN: 10600

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11525 AN: 67994

Other (OTH) AF: 0.268 AC: 565 AN: 2108

Alfa AF: 0.231 Hom.: 11441

Bravo AF: 0.319

Asia WGS AF: 0.316 AC: 1098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.013
DANN	Benign	0.59
PhyloP100		-3.1
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: rs3771863; hg19: chr2-75419714;