rs10517518

Variant names:

• chr4-60929698-G-A
• rs10517518

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 0.112 in 152,110 control chromosomes in the GnomAD database, including 1,906 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 0.11 (1906 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 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: 0.112 AC: 16984 AN: 151992 Hom.: 1888 Cov.: 32

Gnomad AFR AF: 0.0929

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.0940

Gnomad FIN AF: 0.0986

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0602

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.112 AC: 17020 AN: 152110 Hom.: 1906 Cov.: 32 AF XY: 0.120 AC XY: 8924 AN XY: 74352

Gnomad4 AFR AF: 0.0928

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.0937

Gnomad4 FIN AF: 0.0986

Gnomad4 NFE AF: 0.0601

Gnomad4 OTH AF: 0.119

Alfa AF: 0.0673 Hom.: 780

Bravo AF: 0.129

Asia WGS AF: 0.276 AC: 959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.46
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517518; hg19: chr4-61795416;