rs583012

Variant names:

• chr10-53535114-G-A
• rs583012

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 0.755 in 150,184 control chromosomes in the GnomAD database, including 43,970 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 0.76 (43970 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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: 0.755 AC: 113325 AN: 150084 Hom.: 43906 Cov.: 26

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.755 AC: 113440 AN: 150184 Hom.: 43970 Cov.: 26 AF XY: 0.757 AC XY: 55381 AN XY: 73128

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.734

Alfa AF: 0.685 Hom.: 83871

Bravo AF: 0.772

Asia WGS AF: 0.896 AC: 3113 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	2.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs583012; hg19: chr10-55294874;