20-54187830-G-A

Variant names:

• chr20-54187830-G-A
• rs2585422
• ENST00000792273.1:n.289-1530G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000792273.1(ENSG00000286587):​n.289-1530G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 152,276 control chromosomes in the GnomAD database, including 60,141 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 0.89 (60141 hom., cov: 32)
• Consequence: ENSG00000286587 ENST00000792273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456
• Publications: 5 publications found

Genes affected

ENSG00000286587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372675	XR_936882.4	n.275-1530G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286587	ENST00000792273.1	n.289-1530G>A		intron_variant	Intron 3 of 3
ENSG00000286587	ENST00000792274.1	n.455-1530G>A		intron_variant	Intron 5 of 6
ENSG00000286587	ENST00000792275.1	n.336-1765G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134944 AN: 152158 Hom.: 60065 Cov.: 32

Gnomad AFR AF: 0.972

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.887 AC: 135082 AN: 152276 Hom.: 60141 Cov.: 32 AF XY: 0.883 AC XY: 65739 AN XY: 74430

African (AFR) AF: 0.972 AC: 40409 AN: 41576

American (AMR) AF: 0.871 AC: 13333 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2778 AN: 3468

East Asian (EAS) AF: 0.855 AC: 4427 AN: 5176

South Asian (SAS) AF: 0.870 AC: 4206 AN: 4832

European-Finnish (FIN) AF: 0.799 AC: 8445 AN: 10570

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58595 AN: 68026

Other (OTH) AF: 0.871 AC: 1842 AN: 2116

Alfa AF: 0.871 Hom.: 177080

Bravo AF: 0.898

Asia WGS AF: 0.878 AC: 3053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.16
DANN	Benign	0.20
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2585422; hg19: chr20-52804369;