rs10858925

Variant names:

• chr12-89753657-T-A
• rs10858925
• ENST00000546688.1:n.745T>A

Your query was ambiguous. Multiple possible variants found:

• chr12-89753657-T-A
• chr12-89753657-T-C
• chr12-89753657-T-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.745T>A variant causes a non coding transcript exon change. 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: 5.23
• Publications: 7 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=-0.58).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRPL2P1		n.89753657T>A		intragenic_variant
LOC107984543	XR_007063399.1	n.170+36294T>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPL2P1	ENST00000546688.1	n.745T>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ATP2B1-AS1	ENST00000651272.1	n.359+36294T>A		intron_variant	Intron 2 of 6
ENSG00000296746	ENST00000741520.1	n.176-15220A>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 363410 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 204962

African (AFR) AF: 0.00 AC: 0 AN: 10166

American (AMR) AF: 0.00 AC: 0 AN: 30714

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9148

East Asian (EAS) AF: 0.00 AC: 0 AN: 15576

South Asian (SAS) AF: 0.00 AC: 0 AN: 58976

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28102

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2622

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 191132

Other (OTH) AF: 0.00 AC: 0 AN: 16974

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	15
DANN	Benign	0.63
PhyloP100		5.2

Splicing

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

Other links and lift over

dbSNP: rs10858925; hg19: chr12-90147434;