rs2585422

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr20-54187830-G-A
• chr20-54187830-G-C

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792273.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000286587	ENST00000792273.1		n.289-1530G>A		intron	N/A
	ENSG00000286587	ENST00000792274.1		n.455-1530G>A		intron	N/A
	ENSG00000286587	ENST00000792275.1		n.336-1765G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2585422;

hg19: chr20-52804369;