rs2479409

Variant names:

• chr1-55038977-G-A
• rs2479409

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6 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 Conflicting classifications of pathogenicity (no stars).

• Frequency: Genomes: 𝑓 0.65 (33383 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:1 B:1
• Conservation: PhyloP100: -1.28
• Publications: 168 publications found

ACMG classification

Our verdict: Benign. The variant received -13 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 Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 440703.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.740 AC: 30715 AN: 41500

American (AMR) AF: 0.490 AC: 7483 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2170 AN: 3472

East Asian (EAS) AF: 0.341 AC: 1764 AN: 5176

South Asian (SAS) AF: 0.734 AC: 3543 AN: 4826

European-Finnish (FIN) AF: 0.716 AC: 7579 AN: 10588

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44214 AN: 67984

Other (OTH) AF: 0.629 AC: 1329 AN: 2112

Alfa AF: 0.639 Hom.: 105259

Bravo AF: 0.634

Asia WGS AF: 0.576 AC: 2004 AN: 3478

ClinVar

ClinVar submissions

Significance: Conflicting classifications of pathogenicity

Revision: criteria provided, conflicting classifications

Pathogenic	VUS	Benign	Condition
1	-	1	Hypercholesterolemia, familial, 1 (2)
-	1	-	Hypercholesterolemia, autosomal dominant, 3 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.41
DANN	Benign	0.56
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2479409; hg19: chr1-55504650;