rs1905173

chr4-103714945-T-Achr4-103714945-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001059.3(TACR3):c.548+4183A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,146 control chromosomes in the GnomAD database, including 1,357 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 0.12 (1357 hom., cov: 32)
• Consequence: TACR3 NM_001059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

Genes affected

TACR3 (HGNC:11528): (tachykinin receptor 3) This gene belongs to a family of genes that function as receptors for tachykinins. Receptor affinities are specified by variations in the 5'-end of the sequence. The receptors belonging to this family are characterized by interactions with G proteins and 7 hydrophobic transmembrane regions. This gene encodes the receptor for the tachykinin neurokinin 3, also referred to as neurokinin B. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TACR3	NM_001059.3	c.548+4183A>T		intron_variant		ENST00000304883.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TACR3	ENST00000304883.3	c.548+4183A>T		intron_variant		1	NM_001059.3	P1

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17767 AN: 152030 Hom.: 1357 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0871

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.117 AC: 17776 AN: 152146 Hom.: 1357 Cov.: 32 AF XY: 0.125 AC XY: 9278 AN XY: 74372

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.0871

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0447 Hom.: 35

Bravo AF: 0.114

Asia WGS AF: 0.294 AC: 1020 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.9
Dann	Benign	0.70

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: rs1905173; hg19: chr4-104636102;