rs7663664

chr4-103663678-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.549-5275C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,000 control chromosomes in the GnomAD database, including 17,206 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 0.43 (17206 hom., cov: 32)
• Consequence: TACR3 NM_001059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TACR3	NM_001059.3	c.549-5275C>T		intron_variant		ENST00000304883.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TACR3	ENST00000304883.3	c.549-5275C>T		intron_variant		1	NM_001059.3	P1

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65727 AN: 151882 Hom.: 17163 Cov.: 32

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.433 AC: 65822 AN: 152000 Hom.: 17206 Cov.: 32 AF XY: 0.424 AC XY: 31486 AN XY: 74270

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.415

Alfa AF: 0.403 Hom.: 2726

Bravo AF: 0.451

Asia WGS AF: 0.314 AC: 1095 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	0.33
Dann	Benign	0.40

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: rs7663664; hg19: chr4-104584835;