10-87852267-T-C

Variant names:

• chr10-87852267-T-C
• rs11202586

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 152,190 control chromosomes in the GnomAD database, including 2,659 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 (2659 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27201 AN: 152072 Hom.: 2639 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.179 AC: 27263 AN: 152190 Hom.: 2659 Cov.: 32 AF XY: 0.181 AC XY: 13454 AN XY: 74408

African (AFR) AF: 0.123 AC: 5086 AN: 41518

American (AMR) AF: 0.226 AC: 3456 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3470

East Asian (EAS) AF: 0.354 AC: 1834 AN: 5178

South Asian (SAS) AF: 0.181 AC: 874 AN: 4822

European-Finnish (FIN) AF: 0.172 AC: 1826 AN: 10598

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13070 AN: 68004

Other (OTH) AF: 0.200 AC: 421 AN: 2110

Alfa AF: 0.105 Hom.: 190

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	-0.57
CADD	Benign	7.6
DANN	Benign	0.89
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs11202586; hg19: chr10-89612024;