5-52710968-A-G

Variant names:

• chr5-52710968-A-G
• rs183013
• ENST00000502995.1:n.168-25278T>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.168-25278T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.916 in 152,096 control chromosomes in the GnomAD database, including 64,147 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 (64147 hom., cov: 31)
• Consequence: PELO-AS1 ENST00000502995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.807
• Publications: 6 publications found

Genes affected

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

ENSG00000294673 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• 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 rank	MANE	Protein	UniProt
PELO-AS1	NR_186446.1	n.254-25278T>C		intron_variant	Intron 2 of 3
PELO-AS1	NR_186447.1	n.196-25278T>C		intron_variant	Intron 2 of 3
PELO-AS1	NR_186448.1	n.703-19259T>C		intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PELO-AS1	ENST00000502995.1	n.168-25278T>C		intron_variant	Intron 2 of 3	4
PELO-AS1	ENST00000670789.1	n.211-25278T>C		intron_variant	Intron 2 of 3
ENSG00000294673	ENST00000725177.1	n.557+19718A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.916 AC: 139183 AN: 151978 Hom.: 64125 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.974

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.916 AC: 139258 AN: 152096 Hom.: 64147 Cov.: 31 AF XY: 0.917 AC XY: 68129 AN XY: 74334

African (AFR) AF: 0.819 AC: 33975 AN: 41508

American (AMR) AF: 0.892 AC: 13591 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 3361 AN: 3472

East Asian (EAS) AF: 0.817 AC: 4205 AN: 5148

South Asian (SAS) AF: 0.924 AC: 4453 AN: 4820

European-Finnish (FIN) AF: 0.974 AC: 10335 AN: 10610

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.974 AC: 66197 AN: 67982

Other (OTH) AF: 0.923 AC: 1953 AN: 2116

Alfa AF: 0.952 Hom.: 209937

Bravo AF: 0.902

Asia WGS AF: 0.862 AC: 3000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.72
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs183013; hg19: chr5-52006802;