rs10888502

Variant names:

• chr1-152573517-C-G
• rs10888502

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 0.43 in 150,200 control chromosomes in the GnomAD database, including 14,476 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 0.43 (14476 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 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: 0.430 AC: 64566 AN: 150084 Hom.: 14454 Cov.: 27

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.430 AC: 64620 AN: 150200 Hom.: 14476 Cov.: 27 AF XY: 0.428 AC XY: 31328 AN XY: 73246

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.421

Alfa AF: 0.409 Hom.: 1733

Bravo AF: 0.429

Asia WGS AF: 0.362 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10888502; hg19: chr1-152545993;