rs10502578

Variant names:

• chr18-31795124-G-A
• rs10502578

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 0.0819 in 152,238 control chromosomes in the GnomAD database, including 528 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 0.082 (528 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0904 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: 0.0820 AC: 12474 AN: 152120 Hom.: 529 Cov.: 32

Gnomad AFR AF: 0.0797

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0723

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0481

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.0768

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.0850

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.0819 AC: 12475 AN: 152238 Hom.: 528 Cov.: 32 AF XY: 0.0814 AC XY: 6062 AN XY: 74430

Gnomad4 AFR AF: 0.0797

Gnomad4 AMR AF: 0.0722

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.0480

Gnomad4 SAS AF: 0.0977

Gnomad4 FIN AF: 0.0768

Gnomad4 NFE AF: 0.0851

Gnomad4 OTH AF: 0.0928

Alfa AF: 0.0874 Hom.: 875

Bravo AF: 0.0814

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	9.5
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502578; hg19: chr18-29375087;