chr10-87849022-G-C

Variant names:

• chr10-87849022-G-C
• rs11202585

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 0.179 in 151,694 control chromosomes in the GnomAD database, including 2,644 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 (2644 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27063 AN: 151572 Hom.: 2624 Cov.: 30

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.179 AC: 27126 AN: 151694 Hom.: 2644 Cov.: 30 AF XY: 0.180 AC XY: 13344 AN XY: 74078

African (AFR) AF: 0.123 AC: 5073 AN: 41402

American (AMR) AF: 0.225 AC: 3441 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3464

East Asian (EAS) AF: 0.354 AC: 1767 AN: 4998

South Asian (SAS) AF: 0.181 AC: 868 AN: 4804

European-Finnish (FIN) AF: 0.172 AC: 1811 AN: 10508

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.192 AC: 13049 AN: 67932

Other (OTH) AF: 0.199 AC: 421 AN: 2114

Alfa AF: 0.183 Hom.: 329

Bravo AF: 0.181

Asia WGS AF: 0.281 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	5.2
DANN	Benign	0.79
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs11202585; hg19: chr10-89608779; COSMIC: COSV71550661;