rs5082

Variant names:

• chr1-161223893-G-A
• rs5082

Your query was ambiguous. Multiple possible variants found:

• chr1-161223893-G-A
• chr1-161223893-G-C
• chr1-161223893-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP5 BP4 BA1

The variant allele was found at a frequency of 0.68 in 151,986 control chromosomes in the GnomAD database, including 35,682 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: 𝑓 0.68 (35682 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 0.00100

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• PP5: Variant 1-161223893-G-A is Pathogenic according to our data. Variant chr1-161223893-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 17936.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85). . Strength limited to SUPPORTING due to the PP5.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 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: 0.679 AC: 103182 AN: 151868 Hom.: 35628 Cov.: 30

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.680 AC: 103295 AN: 151986 Hom.: 35682 Cov.: 30 AF XY: 0.683 AC XY: 50708 AN XY: 74288

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.668

Alfa AF: 0.627 Hom.: 50448

Bravo AF: 0.694

Asia WGS AF: 0.836 AC: 2900 AN: 3478

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:1

Jan 01, 2002

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5082; hg19: chr1-161193683;