rs10494112

chr1-109809855-A-G

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 0.172 in 152,270 control chromosomes in the GnomAD database, including 2,529 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 0.17 (2529 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.207 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: 0.172 AC: 26107 AN: 152152 Hom.: 2526 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.172 AC: 26126 AN: 152270 Hom.: 2529 Cov.: 33 AF XY: 0.171 AC XY: 12707 AN XY: 74440

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.166

Alfa AF: 0.199 Hom.: 4700

Bravo AF: 0.160

Asia WGS AF: 0.0820 AC: 288 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	6.9
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494112; hg19: chr1-110352477;