rs4745430

Variant names:

• chr9-75657109-C-T
• rs4745430

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;