10-58899073-T-C

Variant names:

• chr10-58899073-T-C
• rs282687

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 0.704 in 152,194 control chromosomes in the GnomAD database, including 40,437 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 0.70 (40437 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 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: 0.704 AC: 107080 AN: 152076 Hom.: 40430 Cov.: 34

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.704 AC: 107118 AN: 152194 Hom.: 40437 Cov.: 34 AF XY: 0.705 AC XY: 52489 AN XY: 74408

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.733

Alfa AF: 0.806 Hom.: 45196

Bravo AF: 0.693

Asia WGS AF: 0.752 AC: 2617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs282687; hg19: chr10-60658833;