chr20-50234655-A-G

Variant names:

• chr20-50234655-A-G
• rs4811011
• ENST00000718352.1:n.118+1122A>G

Variant summary

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

The ENST00000718352.1(PELATON):​n.118+1122A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,984 control chromosomes in the GnomAD database, including 27,445 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 0.59 (27445 hom., cov: 32)
• Consequence: PELATON ENST00000718352.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 3 publications found

Genes affected

PELATON (HGNC:50328): (plaque enriched lncRNA in atherosclerotic and inflammatory bowel macrophage regulation)

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 (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PELATON	ENST00000718352.1	n.118+1122A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89322 AN: 151866 Hom.: 27410 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.588 AC: 89415 AN: 151984 Hom.: 27445 Cov.: 32 AF XY: 0.591 AC XY: 43883 AN XY: 74256

African (AFR) AF: 0.769 AC: 31891 AN: 41484

American (AMR) AF: 0.560 AC: 8554 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1814 AN: 3466

East Asian (EAS) AF: 0.689 AC: 3543 AN: 5144

South Asian (SAS) AF: 0.601 AC: 2894 AN: 4818

European-Finnish (FIN) AF: 0.502 AC: 5301 AN: 10558

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33659 AN: 67940

Other (OTH) AF: 0.578 AC: 1220 AN: 2110

Alfa AF: 0.573 Hom.: 4537

Bravo AF: 0.599

Asia WGS AF: 0.603 AC: 2096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.1
DANN	Benign	0.68
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs4811011; hg19: chr20-48851192;