rs4745430

Variant names:

• chr9-75657109-C-T
• rs4745430

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.720 AC: 29883 AN: 41480

American (AMR) AF: 0.732 AC: 11173 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1946 AN: 3470

East Asian (EAS) AF: 0.881 AC: 4554 AN: 5170

South Asian (SAS) AF: 0.687 AC: 3318 AN: 4830

European-Finnish (FIN) AF: 0.676 AC: 7140 AN: 10558

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43650 AN: 67964

Other (OTH) AF: 0.660 AC: 1393 AN: 2112

Alfa AF: 0.653 Hom.: 52437

Bravo AF: 0.691

Asia WGS AF: 0.736 AC: 2556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.72
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4745430; hg19: chr9-78272025;