rs10520424

Variant names:

• chr4-179343725-G-C
• rs10520424

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 0.349 in 151,930 control chromosomes in the GnomAD database, including 10,028 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 0.35 (10028 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 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: 0.349 AC: 52923 AN: 151808 Hom.: 10003 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.349 AC: 52989 AN: 151930 Hom.: 10028 Cov.: 32 AF XY: 0.357 AC XY: 26492 AN XY: 74252

African (AFR) AF: 0.239 AC: 9908 AN: 41442

American (AMR) AF: 0.502 AC: 7672 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1300 AN: 3468

East Asian (EAS) AF: 0.589 AC: 3034 AN: 5148

South Asian (SAS) AF: 0.471 AC: 2271 AN: 4818

European-Finnish (FIN) AF: 0.365 AC: 3838 AN: 10512

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.353 AC: 23968 AN: 67964

Other (OTH) AF: 0.333 AC: 703 AN: 2108

Alfa AF: 0.370 Hom.: 1330

Bravo AF: 0.352

Asia WGS AF: 0.497 AC: 1729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.5
DANN	Benign	0.67
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs10520424; hg19: chr4-180264879;