rs10917176

chr1-22218804-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;