4-103611793-A-G

Variant names:

• chr4-103611793-A-G
• rs11722288
• NM_001059.3:c.889-20110T>C

Variant summary

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

The NM_001059.3(TACR3):​c.889-20110T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,062 control chromosomes in the GnomAD database, including 39,934 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 0.72 (39934 hom., cov: 32)
• Consequence: TACR3 NM_001059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 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.889-20110T>C		intron	N/A	NP_001050.1	P29371
	TACR3-AS1	NR_186501.1		n.572-12488A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACR3	ENST00000304883.3	TSL:1 MANE Select	c.889-20110T>C		intron	N/A	ENSP00000303325.2	P29371
	TACR3-AS1	ENST00000502936.1	TSL:2	n.572-12488A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109581 AN: 151944 Hom.: 39892 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.721 AC: 109676 AN: 152062 Hom.: 39934 Cov.: 32 AF XY: 0.731 AC XY: 54328 AN XY: 74348

African (AFR) AF: 0.674 AC: 27969 AN: 41472

American (AMR) AF: 0.734 AC: 11205 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2617 AN: 3468

East Asian (EAS) AF: 0.980 AC: 5068 AN: 5170

South Asian (SAS) AF: 0.759 AC: 3658 AN: 4818

European-Finnish (FIN) AF: 0.824 AC: 8720 AN: 10586

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47974 AN: 67968

Other (OTH) AF: 0.707 AC: 1491 AN: 2108

Alfa AF: 0.710 Hom.: 164458

Bravo AF: 0.714

Asia WGS AF: 0.818 AC: 2843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.59
PhyloP100		1.0
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: rs11722288; hg19: chr4-104532950;