rs171288

Variant names:

• chr5-52750270-A-G
• rs171288
• ENST00000502995.1:n.167+35265T>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+35265T>C variant causes a intron 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 ENST00000502995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502995.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PELO-AS1	NR_186446.1		n.253+35265T>C		intron	N/A
	PELO-AS1	NR_186447.1		n.195+35265T>C		intron	N/A
	PELO-AS1	NR_186448.1		n.702+1183T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PELO-AS1	ENST00000502995.1	TSL:4	n.167+35265T>C		intron	N/A
	PELO-AS1	ENST00000670789.1		n.210+35265T>C		intron	N/A

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

African (AFR) AF: 0.104 AC: 4312 AN: 41500

American (AMR) AF: 0.190 AC: 2896 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 629 AN: 3472

East Asian (EAS) AF: 0.217 AC: 1116 AN: 5146

South Asian (SAS) AF: 0.179 AC: 865 AN: 4820

European-Finnish (FIN) AF: 0.125 AC: 1318 AN: 10572

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10874 AN: 67948

Other (OTH) AF: 0.162 AC: 341 AN: 2110

Alfa AF: 0.162 Hom.: 5621

Bravo AF: 0.153

Asia WGS AF: 0.176 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.20
PhyloP100		-0.22

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs171288;

hg19: chr5-52046104;