chr4-103610158-G-A

Variant names:

• chr4-103610158-G-A
• rs1813782
• NM_001059.3:c.889-18475C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001059.3(TACR3):​c.889-18475C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,666 control chromosomes in the GnomAD database, including 22,688 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 0.50 (22688 hom., cov: 31)
• Consequence: TACR3 NM_001059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 0 publications found

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]

TACR3-AS1 (HGNC:55593): (TACR3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001059.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR3	NM_001059.3	MANE Select	c.889-18475C>T		intron	N/A	NP_001050.1	P29371
	TACR3-AS1	NR_186501.1		n.572-14123G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR3	ENST00000304883.3	TSL:1 MANE Select	c.889-18475C>T		intron	N/A	ENSP00000303325.2	P29371
	TACR3-AS1	ENST00000502936.1	TSL:2	n.572-14123G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75206 AN: 151548 Hom.: 22681 Cov.: 31

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.496 AC: 75224 AN: 151666 Hom.: 22688 Cov.: 31 AF XY: 0.502 AC XY: 37199 AN XY: 74106

African (AFR) AF: 0.138 AC: 5711 AN: 41390

American (AMR) AF: 0.587 AC: 8912 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2291 AN: 3468

East Asian (EAS) AF: 0.481 AC: 2470 AN: 5130

South Asian (SAS) AF: 0.458 AC: 2199 AN: 4806

European-Finnish (FIN) AF: 0.758 AC: 7986 AN: 10534

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43705 AN: 67832

Other (OTH) AF: 0.525 AC: 1106 AN: 2108

Alfa AF: 0.441 Hom.: 1523

Bravo AF: 0.472

Asia WGS AF: 0.452 AC: 1573 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.77
DANN	Benign	0.57
PhyloP100		-0.52
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: rs1813782; hg19: chr4-104531315;