rs2245997

Positions:

• chr5-52773663-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.210+11872A>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 0.957 in 152,252 control chromosomes in the GnomAD database, including 69,928 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 (69928 hom., cov: 32)
• Consequence: PELO-AS1 ENST00000670789.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114

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=-0.86).
• 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+11872A>G		intron_variant, non_coding_transcript_variant
PELO-AS1	ENST00000502995.1	n.167+11872A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.957 AC: 145654 AN: 152134 Hom.: 69888 Cov.: 32

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.960

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.957 AC: 145750 AN: 152252 Hom.: 69928 Cov.: 32 AF XY: 0.955 AC XY: 71052 AN XY: 74436

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.971

Gnomad4 ASJ AF: 0.980

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.971

Gnomad4 FIN AF: 0.960

Gnomad4 NFE AF: 0.983

Gnomad4 OTH AF: 0.955

Alfa AF: 0.968 Hom.: 11383

Bravo AF: 0.955

Asia WGS AF: 0.890 AC: 3096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2245997; hg19: chr5-52069497;