rs2798253

Positions:

• chr10-92443148-G-C
• chr10-92443148-G-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;