5-52767845-C-G

Variant names:

• chr5-52767845-C-G
• rs11742611
• ENST00000502995.1:n.167+17690G>C

Variant summary

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

The ENST00000502995.1(PELO-AS1):​n.167+17690G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,924 control chromosomes in the GnomAD database, including 8,584 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 0.30 (8584 hom., cov: 32)
• Consequence: PELO-AS1 ENST00000502995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PELO-AS1	NR_186446.1	n.253+17690G>C		intron_variant	Intron 2 of 3
PELO-AS1	NR_186447.1	n.195+17690G>C		intron_variant	Intron 2 of 3
PELO-AS1	NR_186448.1	n.431-1035G>C		intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PELO-AS1	ENST00000502995.1	n.167+17690G>C		intron_variant	Intron 2 of 3	4
PELO-AS1	ENST00000670789.1	n.210+17690G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45487 AN: 151816 Hom.: 8578 Cov.: 32

Gnomad AFR AF: 0.0852

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.299 AC: 45487 AN: 151924 Hom.: 8584 Cov.: 32 AF XY: 0.300 AC XY: 22296 AN XY: 74234

African (AFR) AF: 0.0850 AC: 3523 AN: 41432

American (AMR) AF: 0.262 AC: 3993 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1577 AN: 3472

East Asian (EAS) AF: 0.144 AC: 746 AN: 5174

South Asian (SAS) AF: 0.296 AC: 1430 AN: 4824

European-Finnish (FIN) AF: 0.459 AC: 4820 AN: 10504

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28409 AN: 67956

Other (OTH) AF: 0.315 AC: 663 AN: 2108

Alfa AF: 0.250 Hom.: 745

Bravo AF: 0.274

Asia WGS AF: 0.229 AC: 797 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.7
DANN	Benign	0.91
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs11742611; hg19: chr5-52063679;