rs10494793

Variant names:

• chr1-199473184-G-A
• rs10494793

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.183 in 151,824 control chromosomes in the GnomAD database, including 2,640 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 0.18 (2640 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.28

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 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: 0.183 AC: 27787 AN: 151704 Hom.: 2636 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.183 AC: 27805 AN: 151824 Hom.: 2640 Cov.: 32 AF XY: 0.185 AC XY: 13722 AN XY: 74218

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.177

Alfa AF: 0.184 Hom.: 4326

Bravo AF: 0.181

Asia WGS AF: 0.254 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	18
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494793; hg19: chr1-199442312;