20-54180142-C-G

Variant names:

• chr20-54180142-C-G
• rs2426498
• ENST00000655028.2:n.666+1654C>G

Variant summary

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

The ENST00000655028.2(ENSG00000286587):​n.666+1654C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,202 control chromosomes in the GnomAD database, including 1,129 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 (1129 hom., cov: 33)
• Consequence: ENSG00000286587 ENST00000655028.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 12 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372675	XR_936882.4	n.195+1654C>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286587	ENST00000655028.2	n.666+1654C>G		intron_variant	Intron 4 of 4
ENSG00000286587	ENST00000792273.1	n.289-9218C>G		intron_variant	Intron 3 of 3
ENSG00000286587	ENST00000792274.1	n.375+1654C>G		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15832 AN: 152084 Hom.: 1128 Cov.: 33

Gnomad AFR AF: 0.0328

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0974

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.104 AC: 15838 AN: 152202 Hom.: 1129 Cov.: 33 AF XY: 0.103 AC XY: 7697 AN XY: 74416

African (AFR) AF: 0.0327 AC: 1360 AN: 41534

American (AMR) AF: 0.0975 AC: 1492 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3472

East Asian (EAS) AF: 0.325 AC: 1680 AN: 5176

South Asian (SAS) AF: 0.117 AC: 566 AN: 4818

European-Finnish (FIN) AF: 0.106 AC: 1120 AN: 10592

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8750 AN: 67990

Other (OTH) AF: 0.115 AC: 244 AN: 2114

Alfa AF: 0.0582 Hom.: 60

Bravo AF: 0.101

Asia WGS AF: 0.163 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.9
DANN	Benign	0.66
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2426498; hg19: chr20-52796681;