rs10502575

Positions:

• chr18-31756628-A-G

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 0.0661 in 152,266 control chromosomes in the GnomAD database, including 694 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 0.066 (694 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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: 0.0661 AC: 10051 AN: 152148 Hom.: 687 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0325

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0202

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0229

Gnomad OTH AF: 0.0636

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

GnomAD4 genome AF: 0.0661 AC: 10069 AN: 152266 Hom.: 694 Cov.: 32 AF XY: 0.0641 AC XY: 4771 AN XY: 74470

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.0324

Gnomad4 ASJ AF: 0.0251

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0263

Gnomad4 FIN AF: 0.0202

Gnomad4 NFE AF: 0.0229

Gnomad4 OTH AF: 0.0629

Alfa AF: 0.0298 Hom.: 159

Bravo AF: 0.0714

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502575; hg19: chr18-29336591;