rs10917176

Variant names:

• chr1-22218804-C-T
• rs10917176

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.198 in 152,018 control chromosomes in the GnomAD database, including 3,506 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 0.20 (3506 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

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: 0.198 AC: 30067 AN: 151900 Hom.: 3503 Cov.: 31

Gnomad AFR AF: 0.0971

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.198 AC: 30078 AN: 152018 Hom.: 3506 Cov.: 31 AF XY: 0.203 AC XY: 15071 AN XY: 74276

Gnomad4 AFR AF: 0.0969

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.203

Alfa AF: 0.202 Hom.: 433

Bravo AF: 0.200

Asia WGS AF: 0.319 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.051
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10917176; hg19: chr1-22545297;