rs10502824

Variant names:

• chr18-44182626-C-T
• rs10502824

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 0.0165 in 152,140 control chromosomes in the GnomAD database, including 125 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 0.016 (125 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.124 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: 0.0164 AC: 2495 AN: 152022 Hom.: 121 Cov.: 32

Gnomad AFR AF: 0.00246

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0857

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00474

Gnomad OTH AF: 0.0173

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

GnomAD4 genome AF: 0.0165 AC: 2508 AN: 152140 Hom.: 125 Cov.: 32 AF XY: 0.0181 AC XY: 1344 AN XY: 74376

Gnomad4 AFR AF: 0.00246

Gnomad4 AMR AF: 0.0866

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.00187

Gnomad4 FIN AF: 0.00283

Gnomad4 NFE AF: 0.00474

Gnomad4 OTH AF: 0.0171

Alfa AF: 0.0176 Hom.: 34

Bravo AF: 0.0261

Asia WGS AF: 0.0390 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.19
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: rs10502824; hg19: chr18-41762591;