rs12521013

chr5-142283799-A-C

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 0.537 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.571

Alfa AF: 0.546 Hom.: 3584

Bravo AF: 0.546

Asia WGS AF: 0.419 AC: 1459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	0.43
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12521013; hg19: chr5-141663364;