rs10520889

Positions:

• chr5-23280811-T-C

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 0.179 in 151,510 control chromosomes in the GnomAD database, including 2,674 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 0.18 (2674 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27075 AN: 151392 Hom.: 2653 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.179 AC: 27135 AN: 151510 Hom.: 2674 Cov.: 32 AF XY: 0.182 AC XY: 13486 AN XY: 74036

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.200

Alfa AF: 0.146 Hom.: 2842

Bravo AF: 0.181

Asia WGS AF: 0.316 AC: 1098 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
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: rs10520889; hg19: chr5-23280920;