ENST00000655028.2:n.667-516G>T

Variant names:

• chr20-54182040-G-T
• rs2585424
• ENST00000655028.2:n.667-516G>T

Variant summary

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

The ENST00000655028.2(ENSG00000286587):​n.667-516G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0821 in 152,282 control chromosomes in the GnomAD database, including 637 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 0.082 (637 hom., cov: 33)
• Consequence: ENSG00000286587 ENST00000655028.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655028.2. 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	ENST00000655028.2		n.667-516G>T		intron	N/A
	ENSG00000286587	ENST00000792273.1		n.289-7320G>T		intron	N/A
	ENSG00000286587	ENST00000792274.1		n.376-516G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0821 AC: 12488 AN: 152164 Hom.: 636 Cov.: 33

Gnomad AFR AF: 0.0517

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0689

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0819

Gnomad OTH AF: 0.0953

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

GnomAD4 genome AF: 0.0821 AC: 12496 AN: 152282 Hom.: 637 Cov.: 33 AF XY: 0.0831 AC XY: 6186 AN XY: 74448

African (AFR) AF: 0.0516 AC: 2146 AN: 41556

American (AMR) AF: 0.105 AC: 1606 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 401 AN: 3472

East Asian (EAS) AF: 0.216 AC: 1120 AN: 5180

South Asian (SAS) AF: 0.139 AC: 671 AN: 4824

European-Finnish (FIN) AF: 0.0689 AC: 730 AN: 10600

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0819 AC: 5572 AN: 68026

Other (OTH) AF: 0.0976 AC: 206 AN: 2110

Alfa AF: 0.0818 Hom.: 872

Bravo AF: 0.0842

Asia WGS AF: 0.185 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.72
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs2585424; hg19: chr20-52798579;