rs10520423

Variant names:

• chr4-179340044-G-A
• rs10520423

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 0.188 in 147,532 control chromosomes in the GnomAD database, including 2,826 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 0.19 (2826 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 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: 0.188 AC: 27690 AN: 147412 Hom.: 2822 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0230

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.273

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.188 AC: 27702 AN: 147532 Hom.: 2826 Cov.: 32 AF XY: 0.183 AC XY: 13163 AN XY: 71736

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.0230

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.183

Alfa AF: 0.226 Hom.: 2202

Bravo AF: 0.176

Asia WGS AF: 0.138 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	5.9
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520423; hg19: chr4-180261198;