chr5-52728758-T-C

Variant names:

• chr5-52728758-T-C
• rs2598324
• ENST00000502995.1:n.168-43068A>G

Variant summary

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

The ENST00000502995.1(PELO-AS1):​n.168-43068A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,162 control chromosomes in the GnomAD database, including 64,909 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 0.92 (64909 hom., cov: 31)
• Consequence: PELO-AS1 ENST00000502995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 2 publications found

Genes affected

PELO-AS1 (HGNC:56263): (PELO antisense RNA 1)

ENSG00000294673 (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 (NFE) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PELO-AS1	NR_186446.1	n.254-43068A>G		intron_variant	Intron 2 of 3
PELO-AS1	NR_186447.1	n.196-43068A>G		intron_variant	Intron 2 of 3
PELO-AS1	NR_186448.1	n.702+22695A>G		intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PELO-AS1	ENST00000502995.1	n.168-43068A>G		intron_variant	Intron 2 of 3	4
PELO-AS1	ENST00000670789.1	n.211-43068A>G		intron_variant	Intron 2 of 3
ENSG00000294673	ENST00000725177.1	n.558-3766T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.922 AC: 140114 AN: 152044 Hom.: 64888 Cov.: 31

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.930

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

GnomAD4 genome AF: 0.921 AC: 140188 AN: 152162 Hom.: 64909 Cov.: 31 AF XY: 0.922 AC XY: 68561 AN XY: 74364

African (AFR) AF: 0.839 AC: 34819 AN: 41502

American (AMR) AF: 0.893 AC: 13628 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 3361 AN: 3472

East Asian (EAS) AF: 0.815 AC: 4192 AN: 5144

South Asian (SAS) AF: 0.924 AC: 4460 AN: 4826

European-Finnish (FIN) AF: 0.974 AC: 10337 AN: 10610

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.974 AC: 66240 AN: 68018

Other (OTH) AF: 0.928 AC: 1963 AN: 2116

Alfa AF: 0.935 Hom.: 10010

Bravo AF: 0.909

Asia WGS AF: 0.862 AC: 2997 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.32
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2598324; hg19: chr5-52024592;