rs6020399

Variant names:

• chr20-50254634-C-T
• rs6020399
• ENST00000651976.1:n.456+1027C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000651976.1(PELATON):​n.456+1027C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00866 in 152,090 control chromosomes in the GnomAD database, including 15 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 0.0087 (15 hom., cov: 33)
• Consequence: PELATON ENST00000651976.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 0 publications found

Genes affected

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

LOC105372656 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00866 (1317/152090) while in subpopulation AFR AF = 0.0299 (1240/41484). AF 95% confidence interval is 0.0285. There are 15 homozygotes in GnomAd4. There are 612 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 15 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372656	XR_936835.3	n.934+1027C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PELATON	ENST00000651976.1	n.456+1027C>T		intron_variant	Intron 3 of 5
PELATON	ENST00000718352.1	n.119-3724C>T		intron_variant	Intron 1 of 4
PELATON	ENST00000718355.1	n.108-3724C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.00863 AC: 1312 AN: 151972 Hom.: 15 Cov.: 33

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00354

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000103

Gnomad OTH AF: 0.00577

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

GnomAD4 genome AF: 0.00866 AC: 1317 AN: 152090 Hom.: 15 Cov.: 33 AF XY: 0.00823 AC XY: 612 AN XY: 74360

African (AFR) AF: 0.0299 AC: 1240 AN: 41484

American (AMR) AF: 0.00354 AC: 54 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5170

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10584

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000103 AC: 7 AN: 67984

Other (OTH) AF: 0.00571 AC: 12 AN: 2100

Alfa AF: 0.00724 Hom.: 2

Bravo AF: 0.00932

Asia WGS AF: 0.00318 AC: 11 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	4.9
DANN	Benign	0.81
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs6020399; hg19: chr20-48871171;