rs583012

Variant names:

• chr10-53535114-G-A
• rs583012

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.925 AC: 37706 AN: 40756

American (AMR) AF: 0.740 AC: 11155 AN: 15080

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2282 AN: 3462

East Asian (EAS) AF: 0.984 AC: 4979 AN: 5060

South Asian (SAS) AF: 0.810 AC: 3841 AN: 4740

European-Finnish (FIN) AF: 0.664 AC: 6654 AN: 10016

Middle Eastern (MID) AF: 0.728 AC: 211 AN: 290

European-Non Finnish (NFE) AF: 0.657 AC: 44549 AN: 67790

Other (OTH) AF: 0.734 AC: 1528 AN: 2082

Alfa AF: 0.700 Hom.: 138357

Bravo AF: 0.772

Asia WGS AF: 0.896 AC: 3113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.68
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs583012; hg19: chr10-55294874;