rs171288

Positions:

• chr5-52750270-A-G

Variant summary

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

The ENST00000670789.1(PELO-AS1):​n.210+35265T>C 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 0.149 in 152,032 control chromosomes in the GnomAD database, including 1,786 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 0.15 (1786 hom., cov: 32)
• Consequence: PELO-AS1 ENST00000670789.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

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 (EAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PELO-AS1	XR_001742662.2	n.155+1183T>C		intron_variant, non_coding_transcript_variant
PELO-AS1	XR_001742661.2	n.158+1183T>C		intron_variant, non_coding_transcript_variant
PELO-AS1	XR_948321.3	n.209+1183T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PELO-AS1	ENST00000670789.1	n.210+35265T>C		intron_variant, non_coding_transcript_variant
PELO-AS1	ENST00000502995.1	n.167+35265T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22596 AN: 151914 Hom.: 1789 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.149 AC: 22588 AN: 152032 Hom.: 1786 Cov.: 32 AF XY: 0.148 AC XY: 11022 AN XY: 74290

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.162

Alfa AF: 0.166 Hom.: 3461

Bravo AF: 0.153

Asia WGS AF: 0.176 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs171288; hg19: chr5-52046104;