rs12521013

Variant names:

• chr5-142283799-A-C
• rs12521013

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 0.537 in 152,026 control chromosomes in the GnomAD database, including 22,155 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 0.54 (22155 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.577 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: 0.537 AC: 81626 AN: 151908 Hom.: 22147 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.537 AC: 81674 AN: 152026 Hom.: 22155 Cov.: 32 AF XY: 0.536 AC XY: 39851 AN XY: 74308

African (AFR) AF: 0.573 AC: 23759 AN: 41444

American (AMR) AF: 0.587 AC: 8978 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2252 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1532 AN: 5168

South Asian (SAS) AF: 0.521 AC: 2514 AN: 4826

European-Finnish (FIN) AF: 0.473 AC: 4988 AN: 10552

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35841 AN: 67968

Other (OTH) AF: 0.571 AC: 1206 AN: 2112

Alfa AF: 0.546 Hom.: 3704

Bravo AF: 0.546

Asia WGS AF: 0.419 AC: 1459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.43
DANN	Benign	0.77
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs12521013; hg19: chr5-141663364;