rs10493928

Variant names:

• chr1-100561702-A-G
• rs10493928

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.105 in 152,140 control chromosomes in the GnomAD database, including 1,006 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 0.11 (1006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 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: 0.105 AC: 16006 AN: 152022 Hom.: 1005 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0874

Gnomad ASJ AF: 0.0589

Gnomad EAS AF: 0.0829

Gnomad SAS AF: 0.0877

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0768

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.105 AC: 16018 AN: 152140 Hom.: 1006 Cov.: 32 AF XY: 0.105 AC XY: 7827 AN XY: 74370

Gnomad4 AFR AF: 0.168 AC: 0.167911 AN: 0.167911

Gnomad4 AMR AF: 0.0876 AC: 0.0875884 AN: 0.0875884

Gnomad4 ASJ AF: 0.0589 AC: 0.0588915 AN: 0.0588915

Gnomad4 EAS AF: 0.0823 AC: 0.0823371 AN: 0.0823371

Gnomad4 SAS AF: 0.0878 AC: 0.087821 AN: 0.087821

Gnomad4 FIN AF: 0.104 AC: 0.104186 AN: 0.104186

Gnomad4 NFE AF: 0.0768 AC: 0.0767861 AN: 0.0767861

Gnomad4 OTH AF: 0.110 AC: 0.109687 AN: 0.109687

Alfa AF: 0.0894 Hom.: 128

Bravo AF: 0.106

Asia WGS AF: 0.104 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	10
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493928; hg19: chr1-101027258;