chr5-52773340-G-A

Position:

• chr5-52773340-G-A

Variant summary

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

The ENST00000670789.1(PELO-AS1):​n.210+12195C>T 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 0.958 in 152,310 control chromosomes in the GnomAD database, including 70,089 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 0.96 (70089 hom., cov: 33)
• Consequence: PELO-AS1 ENST00000670789.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PELO-AS1	ENST00000670789.1	n.210+12195C>T		intron_variant, non_coding_transcript_variant
PELO-AS1	ENST00000502995.1	n.167+12195C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.958 AC: 145857 AN: 152192 Hom.: 70047 Cov.: 33

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.972

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.959

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

GnomAD4 genome AF: 0.958 AC: 145957 AN: 152310 Hom.: 70089 Cov.: 33 AF XY: 0.956 AC XY: 71170 AN XY: 74474

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.972

Gnomad4 ASJ AF: 0.980

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.971

Gnomad4 FIN AF: 0.961

Gnomad4 NFE AF: 0.983

Gnomad4 OTH AF: 0.956

Alfa AF: 0.974 Hom.: 8966

Bravo AF: 0.956

Asia WGS AF: 0.893 AC: 3103 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2245991; hg19: chr5-52069174;