chr12-89753487-C-A

Variant names:

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

Variant summary

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

The ENST00000546688.1(MRPL2P1):​n.575C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 550,976 control chromosomes in the GnomAD database, including 123,216 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 0.67 (34276 hom., cov: 31)
  • Exomes 𝑓: 0.66 (88940 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101266 AN: 151840 Hom.: 34247 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.681

GnomAD4 exome AF: 0.655 AC: 261470 AN: 399018 Hom.: 88940 Cov.: 4 AF XY: 0.671 AC XY: 145752 AN XY: 217148

African (AFR) AF: 0.506 AC: 5167 AN: 10218

American (AMR) AF: 0.541 AC: 12966 AN: 23952

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 5862 AN: 7970

East Asian (EAS) AF: 0.778 AC: 11399 AN: 14650

South Asian (SAS) AF: 0.805 AC: 39701 AN: 49298

European-Finnish (FIN) AF: 0.587 AC: 18791 AN: 32022

Middle Eastern (MID) AF: 0.694 AC: 1737 AN: 2504

European-Non Finnish (NFE) AF: 0.639 AC: 153521 AN: 240166

Other (OTH) AF: 0.676 AC: 12326 AN: 18238

GnomAD4 genome AF: 0.667 AC: 101340 AN: 151958 Hom.: 34276 Cov.: 31 AF XY: 0.662 AC XY: 49189 AN XY: 74256

African (AFR) AF: 0.576 AC: 23850 AN: 41414

American (AMR) AF: 0.606 AC: 9248 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2603 AN: 3468

East Asian (EAS) AF: 0.813 AC: 4205 AN: 5172

South Asian (SAS) AF: 0.814 AC: 3912 AN: 4808

European-Finnish (FIN) AF: 0.588 AC: 6205 AN: 10544

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48945 AN: 67970

Other (OTH) AF: 0.685 AC: 1446 AN: 2112

Alfa AF: 0.575 Hom.: 1526

Bravo AF: 0.666

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	13
DANN	Benign	0.71
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; COSMIC: COSV72764355;