rs10502578

Positions:

• chr18-31795124-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 0.0819 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;