rs12902499

Variant names:

• chr15-41294945-C-T
• rs12902499
• ENST00000661438.1:c.-803+8845C>T

Variant summary

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

The ENST00000661438.1(ENSG00000285920):​c.-803+8845C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0402 in 152,206 control chromosomes in the GnomAD database, including 223 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 0.040 (223 hom., cov: 31)
• Consequence: ENSG00000285920 ENST00000661438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 2 publications found

Genes affected

ENSG00000285920 (HGNC:):

OIP5-AS1 (HGNC:43563): (OIP5 antisense RNA 1) This is a conserved gene that produces a long non-coding RNA that maintains cell proliferation in embryonic stem cells. This RNA can bind to and negatively regulate the activity of multiple cellular RNAs and microRNAs, including cyclin G associated kinase and ELAV like RNA binding protein 1. [provided by RefSeq, Dec 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0575 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661438.1. 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
	OIP5-AS1	NR_026757.2		n.351-3096C>T		intron	N/A
	OIP5-AS1	NR_152820.1		n.113-3096C>T		intron	N/A
	OIP5-AS1	NR_152821.1		n.112+8845C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285920	ENST00000661438.1		c.-803+8845C>T		intron	N/A	ENSP00000499503.1
	OIP5-AS1	ENST00000500949.7	TSL:1	n.383-3096C>T		intron	N/A
	OIP5-AS1	ENST00000707015.1		n.574C>T		non_coding_transcript_exon	Exon 4 of 5

Frequencies

GnomAD3 genomes AF: 0.0402 AC: 6120 AN: 152088 Hom.: 223 Cov.: 31

Gnomad AFR AF: 0.00891

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0202

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0590

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0402 AC: 6114 AN: 152206 Hom.: 223 Cov.: 31 AF XY: 0.0399 AC XY: 2971 AN XY: 74412

African (AFR) AF: 0.00889 AC: 369 AN: 41524

American (AMR) AF: 0.0201 AC: 307 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.0131 AC: 63 AN: 4826

European-Finnish (FIN) AF: 0.106 AC: 1120 AN: 10604

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0590 AC: 4012 AN: 68006

Other (OTH) AF: 0.0241 AC: 51 AN: 2114

Alfa AF: 0.0524 Hom.: 30

Bravo AF: 0.0322

Asia WGS AF: 0.00779 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.92
DANN	Benign	0.70
PhyloP100		-0.14

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: rs12902499;

hg19: chr15-41587143;