10-58899073-T-C

Variant names:

• chr10-58899073-T-C
• rs282687

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.405 AC: 16813 AN: 41504

American (AMR) AF: 0.822 AC: 12578 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2763 AN: 3472

East Asian (EAS) AF: 0.874 AC: 4531 AN: 5184

South Asian (SAS) AF: 0.679 AC: 3275 AN: 4826

European-Finnish (FIN) AF: 0.807 AC: 8552 AN: 10598

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56165 AN: 67998

Other (OTH) AF: 0.733 AC: 1549 AN: 2112

Alfa AF: 0.789 Hom.: 58228

Bravo AF: 0.693

Asia WGS AF: 0.752 AC: 2617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.65
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs282687; hg19: chr10-60658833;