10-92443148-G-C

Variant names:

• chr10-92443148-G-C
• rs2798253

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 0.654 in 151,476 control chromosomes in the GnomAD database, including 33,420 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 0.65 (33420 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.976

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 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: 0.654 AC: 98996 AN: 151356 Hom.: 33388 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.654 AC: 99089 AN: 151476 Hom.: 33420 Cov.: 32 AF XY: 0.650 AC XY: 48062 AN XY: 73908

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.642

Alfa AF: 0.657 Hom.: 4171

Bravo AF: 0.665

Asia WGS AF: 0.471 AC: 1639 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	0.22
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2798253; hg19: chr10-94202905;