rs10517518

Variant names:

• chr4-60929698-G-A
• rs10517518

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 0.112 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0928 AC: 3850 AN: 41502

American (AMR) AF: 0.311 AC: 4751 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3468

East Asian (EAS) AF: 0.470 AC: 2420 AN: 5144

South Asian (SAS) AF: 0.0937 AC: 452 AN: 4824

European-Finnish (FIN) AF: 0.0986 AC: 1043 AN: 10578

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0601 AC: 4089 AN: 68004

Other (OTH) AF: 0.119 AC: 250 AN: 2106

Alfa AF: 0.0735 Hom.: 1373

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
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs10517518; hg19: chr4-61795416;