rs10516202

Variant names:

• chr4-10124321-C-G
• rs10516202

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 0.111 in 152,214 control chromosomes in the GnomAD database, including 1,302 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 0.11 (1302 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 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: 0.111 AC: 16930 AN: 152096 Hom.: 1297 Cov.: 34

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0720

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0669

Gnomad OTH AF: 0.0972

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

GnomAD4 genome AF: 0.111 AC: 16956 AN: 152214 Hom.: 1302 Cov.: 34 AF XY: 0.115 AC XY: 8579 AN XY: 74420

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.0579

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.0720

Gnomad4 NFE AF: 0.0669

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0853 Hom.: 74

Bravo AF: 0.121

Asia WGS AF: 0.251 AC: 872 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	0.75
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516202; hg19: chr4-10125945;