rs583012

Positions:

• chr10-53535114-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 0.755 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;