rs10518581

Variant names:

• chr4-130952417-C-G
• rs10518581

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 0.41 in 151,052 control chromosomes in the GnomAD database, including 13,307 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 0.41 (13307 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 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: 0.410 AC: 61838 AN: 150936 Hom.: 13304 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.425

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.410 AC: 61870 AN: 151052 Hom.: 13307 Cov.: 31 AF XY: 0.404 AC XY: 29847 AN XY: 73794

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.380

Alfa AF: 0.433 Hom.: 1774

Bravo AF: 0.399

Asia WGS AF: 0.240 AC: 819 AN: 3408

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.33
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518581; hg19: chr4-131873572;