rs58857981

Variant names:

• chr19-41857210-A-G
• rs58857981

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 0.417 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.161 AC: 6662 AN: 41480

American (AMR) AF: 0.491 AC: 7488 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2123 AN: 3460

East Asian (EAS) AF: 0.459 AC: 2355 AN: 5128

South Asian (SAS) AF: 0.572 AC: 2750 AN: 4808

European-Finnish (FIN) AF: 0.515 AC: 5430 AN: 10542

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34818 AN: 67918

Other (OTH) AF: 0.471 AC: 988 AN: 2096

Alfa AF: 0.457 Hom.: 2099

Bravo AF: 0.401

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.0
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs58857981; hg19: chr19-42361281;