rs4580655

chr4-103608117-G-A

Variant summary

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

The NM_001059.3(TACR3):c.889-16434C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 151,890 control chromosomes in the GnomAD database, including 29,932 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 0.62 (29932 hom., cov: 32)
• Consequence: TACR3 NM_001059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TACR3	NM_001059.3	c.889-16434C>T		intron_variant		ENST00000304883.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TACR3	ENST00000304883.3	c.889-16434C>T		intron_variant		1	NM_001059.3	P1
TACR3-AS1	ENST00000502936.1	n.571+14685G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94830 AN: 151772 Hom.: 29904 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.625 AC: 94900 AN: 151890 Hom.: 29932 Cov.: 32 AF XY: 0.625 AC XY: 46409 AN XY: 74238

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.758

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.621

Alfa AF: 0.638 Hom.: 5294

Bravo AF: 0.618

Asia WGS AF: 0.480 AC: 1671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.4
Dann	Benign	0.38

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: rs4580655; hg19: chr4-104529274;