rs10833583

Positions:

• chr11-21647747-G-A

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 0.0969 in 152,104 control chromosomes in the GnomAD database, including 893 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 0.097 (893 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.126 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: 0.0970 AC: 14738 AN: 151988 Hom.: 893 Cov.: 31

Gnomad AFR AF: 0.0284

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0969 AC: 14734 AN: 152104 Hom.: 893 Cov.: 31 AF XY: 0.0981 AC XY: 7294 AN XY: 74318

Gnomad4 AFR AF: 0.0284

Gnomad4 AMR AF: 0.0769

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.100

Alfa AF: 0.122 Hom.: 1154

Bravo AF: 0.0876

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10833583; hg19: chr11-21669293;