rs477558

Variant names:

• chr1-17893333-G-A
• rs477558

Your query was ambiguous. Multiple possible variants found:

• chr1-17893333-G-A
• chr1-17893333-G-C

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 0.542 in 151,798 control chromosomes in the GnomAD database, including 22,855 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 0.54 (22855 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 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: 0.542 AC: 82215 AN: 151680 Hom.: 22840 Cov.: 30

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.628

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.542 AC: 82258 AN: 151798 Hom.: 22855 Cov.: 30 AF XY: 0.542 AC XY: 40162 AN XY: 74146

African (AFR) AF: 0.461 AC: 19074 AN: 41370

American (AMR) AF: 0.694 AC: 10597 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2194 AN: 3472

East Asian (EAS) AF: 0.759 AC: 3903 AN: 5142

South Asian (SAS) AF: 0.496 AC: 2382 AN: 4804

European-Finnish (FIN) AF: 0.470 AC: 4943 AN: 10508

Middle Eastern (MID) AF: 0.624 AC: 181 AN: 290

European-Non Finnish (NFE) AF: 0.549 AC: 37263 AN: 67916

Other (OTH) AF: 0.574 AC: 1210 AN: 2108

Alfa AF: 0.554 Hom.: 46148

Bravo AF: 0.561

Asia WGS AF: 0.610 AC: 2120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.77
PhyloP100		0.034

Splicing

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

Other links and lift over

dbSNP: rs477558; hg19: chr1-18219827;