10-58833048-A-G

Position:

• chr10-58833048-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 0.79 in 152,114 control chromosomes in the GnomAD database, including 50,271 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 0.79 (50271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.916 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: 0.790 AC: 120113 AN: 151996 Hom.: 50262 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.790 AC: 120155 AN: 152114 Hom.: 50271 Cov.: 32 AF XY: 0.790 AC XY: 58778 AN XY: 74366

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.885

Gnomad4 ASJ AF: 0.968

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.922

Gnomad4 OTH AF: 0.808

Alfa AF: 0.863 Hom.: 9709

Bravo AF: 0.778

Asia WGS AF: 0.796 AC: 2771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.6
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7098555; hg19: chr10-60592808;