rs78052302

chr2-75053594-C-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001058.4(TACR1):c.735+11G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000704 in 1,514,460 control chromosomes in the GnomAD database, including 5 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 0.00062 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00071 (5 hom.)
• Consequence: TACR1 NM_001058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.754

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

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BS2: High Homozygotes in GnomAdExome at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TACR1	NM_001058.4	c.735+11G>T		intron_variant		ENST00000305249.10
TACR1	NM_015727.3	c.735+11G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TACR1	ENST00000305249.10	c.735+11G>T		intron_variant		1	NM_001058.4	P1
TACR1	ENST00000409848.3	c.735+11G>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.000627 AC: 90 AN: 143614 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000123

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000207

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000677

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00125

Gnomad OTH AF: 0.000520

GnomAD3 exomes AF: 0.000752 AC: 130 AN: 172924 Hom.: 2 AF XY: 0.000770 AC XY: 70 AN XY: 90906

Gnomad AFR exome AF: 0.0000697

Gnomad AMR exome AF: 0.000663

Gnomad ASJ exome AF: 0.000230

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00123

Gnomad FIN exome AF: 0.000289

Gnomad NFE exome AF: 0.00108

Gnomad OTH exome AF: 0.000774

GnomAD4 exome AF: 0.000713 AC: 977 AN: 1370728 Hom.: 5 Cov.: 30 AF XY: 0.000729 AC XY: 490 AN XY: 672590

Gnomad4 AFR exome AF: 0.0000662

Gnomad4 AMR exome AF: 0.000654

Gnomad4 ASJ exome AF: 0.000339

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00148

Gnomad4 FIN exome AF: 0.000239

Gnomad4 NFE exome AF: 0.000748

Gnomad4 OTH exome AF: 0.000568

GnomAD4 genome AF: 0.000619 AC: 89 AN: 143732 Hom.: 0 Cov.: 32 AF XY: 0.000638 AC XY: 45 AN XY: 70528

Gnomad4 AFR AF: 0.000122

Gnomad4 AMR AF: 0.000207

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000678

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00124

Gnomad4 OTH AF: 0.000514

Alfa AF: 0.00142 Hom.: 1

Bravo AF: 0.000465

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	5.6
Dann	Benign	0.78

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: rs78052302; hg19: chr2-75280721;