chr20-54186450-T-C

Variant names:

• chr20-54186450-T-C
• rs2585423
• ENST00000792273.1:n.289-2910T>C

Variant summary

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

The ENST00000792273.1(ENSG00000286587):​n.289-2910T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,138 control chromosomes in the GnomAD database, including 966 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 0.10 (966 hom., cov: 32)
• Consequence: ENSG00000286587 ENST00000792273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325
• Publications: 4 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286587	ENST00000792273.1		n.289-2910T>C		intron	N/A
	ENSG00000286587	ENST00000792274.1		n.455-2910T>C		intron	N/A
	ENSG00000286587	ENST00000792275.1		n.336-3145T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15417 AN: 152018 Hom.: 965 Cov.: 32

Gnomad AFR AF: 0.0331

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.101 AC: 15423 AN: 152138 Hom.: 966 Cov.: 32 AF XY: 0.103 AC XY: 7647 AN XY: 74374

African (AFR) AF: 0.0330 AC: 1371 AN: 41512

American (AMR) AF: 0.136 AC: 2074 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 464 AN: 3468

East Asian (EAS) AF: 0.219 AC: 1129 AN: 5158

South Asian (SAS) AF: 0.150 AC: 724 AN: 4822

European-Finnish (FIN) AF: 0.103 AC: 1093 AN: 10580

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8253 AN: 68002

Other (OTH) AF: 0.112 AC: 237 AN: 2110

Alfa AF: 0.116 Hom.: 3436

Bravo AF: 0.102

Asia WGS AF: 0.194 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.63
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2585423; hg19: chr20-52802989;