rs12902499

Positions:

• chr15-41294945-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_152821.1(OIP5-AS1):​n.112+8845C>T variant causes a intron, non coding transcript 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: OIP5-AS1 NR_152821.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

Genes affected

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OIP5-AS1	NR_152821.1	n.112+8845C>T		intron_variant, non_coding_transcript_variant
OIP5-AS1	NR_026757.2	n.351-3096C>T		intron_variant, non_coding_transcript_variant
OIP5-AS1	NR_152820.1	n.113-3096C>T		intron_variant, non_coding_transcript_variant
OIP5-AS1	NR_152822.1	n.351-2802C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OIP5-AS1	ENST00000707047.1	n.343+8845C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00889

Gnomad4 AMR AF: 0.0201

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0131

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0590

Gnomad4 OTH AF: 0.0241

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12902499; hg19: chr15-41587143;