20-54084754-C-T

Variant names:

• chr20-54084754-C-T
• rs6064045
• ENST00000792273.1:n.57+25578C>T

Variant summary

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

The ENST00000792273.1(ENSG00000286587):​n.57+25578C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 152,142 control chromosomes in the GnomAD database, including 14,736 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 0.42 (14736 hom., cov: 33)
• Consequence: ENSG00000286587 ENST00000792273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.19
• Publications: 8 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.568 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.57+25578C>T		intron	N/A
	ENSG00000286587	ENST00000792274.1		n.47+25578C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63551 AN: 152022 Hom.: 14728 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.418 AC: 63574 AN: 152142 Hom.: 14736 Cov.: 33 AF XY: 0.416 AC XY: 30921 AN XY: 74390

African (AFR) AF: 0.237 AC: 9827 AN: 41496

American (AMR) AF: 0.578 AC: 8839 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1620 AN: 3472

East Asian (EAS) AF: 0.265 AC: 1373 AN: 5182

South Asian (SAS) AF: 0.376 AC: 1812 AN: 4824

European-Finnish (FIN) AF: 0.404 AC: 4275 AN: 10572

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

European-Non Finnish (NFE) AF: 0.501 AC: 34063 AN: 67988

Other (OTH) AF: 0.482 AC: 1020 AN: 2114

Alfa AF: 0.480 Hom.: 76186

Bravo AF: 0.428

Asia WGS AF: 0.302 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0030
DANN	Benign	0.47
PhyloP100		-3.2

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: rs6064045;

hg19: chr20-52701293;