rs2479409

Positions:

• chr1-55038977-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.655 in 152,146 control chromosomes in the GnomAD database, including 33,383 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.65 (33383 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter P:1 B:1
• Conservation: PhyloP100: -1.28

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 1-55038977-G-A is Benign according to our data. Variant chr1-55038977-G-A is described in ClinVar as [Benign]. Clinvar id is 440703.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-55038977-G-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.55038977G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99579 AN: 152028 Hom.: 33358 Cov.: 33

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.655 AC: 99648 AN: 152146 Hom.: 33383 Cov.: 33 AF XY: 0.654 AC XY: 48676 AN XY: 74388

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.629

Alfa AF: 0.635 Hom.: 60428

Bravo AF: 0.634

Asia WGS AF: 0.576 AC: 2004 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Pathogenic:1 Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:1 Benign:1

Pathogenic, no assertion criteria provided	research	Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	-	- -
Benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Aug 23, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.41
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2479409; hg19: chr1-55504650;