12-89753487-C-G

Variant names:

• chr12-89753487-C-G
• rs882968
• ENST00000546688.1:n.575C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000546688.1(MRPL2P1):​n.575C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MRPL2P1 ENST00000546688.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.44
• Publications: 2 publications found

Genes affected

MRPL2P1 (HGNC:29698): (mitochondrial ribosomal protein L2 pseudogene 1)

ATP2B1-AS1 (HGNC:27883): (ATP2B1 antisense RNA 1)

ENSG00000296746 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546688.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRPL2P1	ENST00000546688.1	TSL:6	n.575C>G		non_coding_transcript_exon	Exon 1 of 1
	ATP2B1-AS1	ENST00000651272.1		n.359+36124C>G		intron	N/A
	ENSG00000296746	ENST00000741520.1		n.176-15050G>C		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 405156 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 220268

African (AFR) AF: 0.00 AC: 0 AN: 10362

American (AMR) AF: 0.00 AC: 0 AN: 24086

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8058

East Asian (EAS) AF: 0.00 AC: 0 AN: 14738

South Asian (SAS) AF: 0.00 AC: 0 AN: 49454

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32224

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2534

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 245202

Other (OTH) AF: 0.00 AC: 0 AN: 18498

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	13
DANN	Benign	0.57
PhyloP100		3.4

Splicing

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

Other links and lift over

dbSNP: rs882968; hg19: chr12-90147264;