rs10883533

chr10-100712899-G-Cchr10-100712899-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 0.379 in 151,944 control chromosomes in the GnomAD database, including 13,112 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 0.38 (13112 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 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: 0.379 AC: 57541 AN: 151826 Hom.: 13116 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.379 AC: 57551 AN: 151944 Hom.: 13112 Cov.: 31 AF XY: 0.394 AC XY: 29266 AN XY: 74266

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.951

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.372

Alfa AF: 0.391 Hom.: 1574

Bravo AF: 0.360

Asia WGS AF: 0.679 AC: 2358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	6.3
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10883533; hg19: chr10-102472656;