rs58857981

Variant names:

• chr19-41857210-A-G
• rs58857981

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 0.417 in 151,874 control chromosomes in the GnomAD database, including 15,201 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 0.42 (15201 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.554 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: 0.417 AC: 63322 AN: 151756 Hom.: 15203 Cov.: 30

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.417 AC: 63326 AN: 151874 Hom.: 15201 Cov.: 30 AF XY: 0.422 AC XY: 31350 AN XY: 74224

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.471

Alfa AF: 0.457 Hom.: 2099

Bravo AF: 0.401

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs58857981; hg19: chr19-42361281;