rs4745430

chr9-75657109-C-T

Variant summary

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

The variant allele was found at a frequency of 0.682 in 152,062 control chromosomes in the GnomAD database, including 35,646 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 0.68 (35646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103674 AN: 151944 Hom.: 35628 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.682 AC: 103735 AN: 152062 Hom.: 35646 Cov.: 32 AF XY: 0.686 AC XY: 50997 AN XY: 74330

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.660

Alfa AF: 0.648 Hom.: 40660

Bravo AF: 0.691

Asia WGS AF: 0.736 AC: 2556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.4
Dann	Benign	0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4745430; hg19: chr9-78272025;