rs3771863

chr2-75192588-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC105374811 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TACR1	NM_001058.4	c.389+5958G>A		intron_variant		ENST00000305249.10
LOC105374811	NR_168009.1	n.372+36273C>T		intron_variant, non_coding_transcript_variant
TACR1	NM_015727.3	c.389+5958G>A		intron_variant
LOC105374811	NR_168010.1	n.366+36273C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TACR1	ENST00000305249.10	c.389+5958G>A		intron_variant		1	NM_001058.4	P1
TACR1	ENST00000409848.3	c.389+5958G>A		intron_variant		1

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

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.268

Alfa AF: 0.223 Hom.: 2572

Bravo AF: 0.319

Asia WGS AF: 0.316 AC: 1098 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	0.013
Dann	Benign	0.59

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

Publications

LitVar

Other links and lift over

dbSNP: rs3771863; hg19: chr2-75419714;