rs2245991

Variant names:

• chr5-52773340-G-A
• rs2245991
• ENST00000502995.1:n.167+12195C>T

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+12195C>T variant causes a intron 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 ENST00000502995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• 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=-0.91).
• 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 rank	MANE	Protein	UniProt
PELO-AS1	NR_186446.1	n.253+12195C>T		intron_variant	Intron 2 of 3
PELO-AS1	NR_186447.1	n.195+12195C>T		intron_variant	Intron 2 of 3
PELO-AS1	NR_186448.1	n.254-2724C>T		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PELO-AS1	ENST00000502995.1	n.167+12195C>T		intron_variant	Intron 2 of 3	4
PELO-AS1	ENST00000670789.1	n.210+12195C>T		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.930 AC: 38663 AN: 41554

American (AMR) AF: 0.972 AC: 14865 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3399 AN: 3470

East Asian (EAS) AF: 0.777 AC: 4021 AN: 5176

South Asian (SAS) AF: 0.971 AC: 4692 AN: 4832

European-Finnish (FIN) AF: 0.961 AC: 10205 AN: 10620

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.983 AC: 66915 AN: 68042

Other (OTH) AF: 0.956 AC: 2020 AN: 2114

Alfa AF: 0.973 Hom.: 9313

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
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs2245991; hg19: chr5-52069174;