4-103696031-G-C

Position:

• chr4-103696031-G-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+23097C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 151,468 control chromosomes in the GnomAD database, including 1,478 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 (1478 hom., cov: 32)
• Consequence: TACR3 NM_001059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TACR3	NM_001059.3	c.548+23097C>G		intron_variant		ENST00000304883.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TACR3	ENST00000304883.3	c.548+23097C>G		intron_variant		1	NM_001059.3	P1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18022 AN: 151352 Hom.: 1478 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.0874

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.119 AC: 18035 AN: 151468 Hom.: 1478 Cov.: 32 AF XY: 0.127 AC XY: 9410 AN XY: 73980

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.0873

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0934 Hom.: 98

Bravo AF: 0.117

Asia WGS AF: 0.304 AC: 1052 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.75
DANN	Benign	0.39

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: rs11097824; hg19: chr4-104617188;