rs10508217

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 22 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0192

Gnomad4 AMR AF: 0.0119

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.0344

Gnomad4 SAS AF: 0.0385

Gnomad4 FIN AF: 0.00208

Gnomad4 NFE AF: 0.0144

Gnomad4 OTH AF: 0.0189

Alfa AF: 0.00475 Hom.: 0

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508217; hg19: chr10-1838859;