rs10508217

Variant names:

• chr10-1796665-C-A
• rs10508217

Your query was ambiguous. Multiple possible variants found:

• chr10-1796665-C-A
• chr10-1796665-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0161 in 152,230 control chromosomes in the GnomAD database, including 22 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 0.016 (22 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0161 (2453/152230) while in subpopulation SAS AF = 0.0385 (186/4826). AF 95% confidence interval is 0.034. There are 22 homozygotes in GnomAd4. There are 1193 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 22 gene

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: 0.0161 AC: 2453 AN: 152112 Hom.: 22 Cov.: 33

Gnomad AFR AF: 0.0191

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0119

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.0345

Gnomad SAS AF: 0.0389

Gnomad FIN AF: 0.00208

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0144

Gnomad OTH AF: 0.0191

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

GnomAD4 genome AF: 0.0161 AC: 2453 AN: 152230 Hom.: 22 Cov.: 33 AF XY: 0.0160 AC XY: 1193 AN XY: 74434

African (AFR) AF: 0.0192 AC: 796 AN: 41532

American (AMR) AF: 0.0119 AC: 182 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3470

East Asian (EAS) AF: 0.0344 AC: 178 AN: 5170

South Asian (SAS) AF: 0.0385 AC: 186 AN: 4826

European-Finnish (FIN) AF: 0.00208 AC: 22 AN: 10598

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0144 AC: 977 AN: 68020

Other (OTH) AF: 0.0189 AC: 40 AN: 2112

Alfa AF: 0.00622 Hom.: 1

Bravo AF: 0.0173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.62
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs10508217; hg19: chr10-1838859;