10-100712899-G-C

Variant names:

• chr10-100712899-G-C
• rs10883533

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;