chr5-142283799-A-C

Variant names:

• chr5-142283799-A-C
• rs12521013

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;