rs10502525

Positions:

• chr18-29085706-G-A

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 0.783 in 151,942 control chromosomes in the GnomAD database, including 46,970 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 0.78 (46970 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118836 AN: 151824 Hom.: 46940 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.783 AC: 118920 AN: 151942 Hom.: 46970 Cov.: 32 AF XY: 0.783 AC XY: 58125 AN XY: 74242

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.851

Gnomad4 ASJ AF: 0.888

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.786

Gnomad4 FIN AF: 0.769

Gnomad4 NFE AF: 0.817

Gnomad4 OTH AF: 0.826

Alfa AF: 0.805 Hom.: 23625

Bravo AF: 0.790

Asia WGS AF: 0.870 AC: 3028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.57
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502525; hg19: chr18-26665670;