rs10794792

chr10-1854361-G-Achr10-1854361-G-C

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 0.578 in 151,944 control chromosomes in the GnomAD database, including 26,525 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 0.58 (26525 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133

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 = 0.67 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: 0.578 AC: 87827 AN: 151826 Hom.: 26509 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.578 AC: 87892 AN: 151944 Hom.: 26525 Cov.: 32 AF XY: 0.580 AC XY: 43086 AN XY: 74256

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.594

Alfa AF: 0.650 Hom.: 17231

Bravo AF: 0.565

Asia WGS AF: 0.572 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.5
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10794792; hg19: chr10-1896555;