Genetic Variant MRPL2P1:n.575C>G (chr12-89753487-C-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.44

Publications

2 publications found

Variant links:

Genes affected

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

MRPL2P1 links:

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

ATP2B1-AS1 links:

ENSG00000296746 (HGNC:):

ENSG00000296746 links:

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new If you want to explore the variant's impact on the transcript ENST00000546688.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
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.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

405156

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

220268

African (AFR)

AF:

0.00

AC:

AN:

10362

American (AMR)

AF:

0.00

AC:

AN:

24086

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

8058

East Asian (EAS)

AF:

0.00

AC:

AN:

14738

South Asian (SAS)

AF:

0.00

AC:

AN:

49454

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32224

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2534

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

245202

Other (OTH)

AF:

0.00

AC:

AN:

18498

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

(source)

DANN

Benign

0.57

PhyloP100

3.4

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.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over