5-52728758-T-C

Position:

• chr5-52728758-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000670789.1(PELO-AS1):​n.211-43068A>G variant causes a intron, non coding transcript 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 ENST00000670789.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
PELO-AS1	XR_001742662.2	n.156-18514A>G		intron_variant, non_coding_transcript_variant
PELO-AS1	XR_001742661.2	n.159-18514A>G		intron_variant, non_coding_transcript_variant
PELO-AS1	XR_948321.3	n.210-18514A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PELO-AS1	ENST00000670789.1	n.211-43068A>G		intron_variant, non_coding_transcript_variant
PELO-AS1	ENST00000502995.1	n.168-43068A>G		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.968

Gnomad4 EAS AF: 0.815

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.974

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.928

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2598324; hg19: chr5-52024592;