rs5082

chr1-161223893-G-Achr1-161223893-G-Cchr1-161223893-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 01, 2002

- -

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;