12-89753657-T-C

Variant names:

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

Variant summary

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

The ENST00000546688.1(MRPL2P1):​n.745T>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.695 in 514,632 control chromosomes in the GnomAD database, including 126,004 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 (34281 hom., cov: 31)
  • Exomes 𝑓: 0.71 (91723 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.792 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

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.745T>C		non_coding_transcript_exon	Exon 1 of 1
	ATP2B1-AS1	ENST00000651272.1		n.359+36294T>C		intron	N/A
	ENSG00000296746	ENST00000741520.1		n.176-15220A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101285 AN: 151878 Hom.: 34252 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.750

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: 0.706 AC: 256103 AN: 362636 Hom.: 91723 Cov.: 0 AF XY: 0.720 AC XY: 147202 AN XY: 204532

African (AFR) AF: 0.561 AC: 5689 AN: 10142

American (AMR) AF: 0.551 AC: 16890 AN: 30628

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 6941 AN: 9128

East Asian (EAS) AF: 0.798 AC: 12407 AN: 15554

South Asian (SAS) AF: 0.811 AC: 47762 AN: 58904

European-Finnish (FIN) AF: 0.593 AC: 16573 AN: 27944

Middle Eastern (MID) AF: 0.709 AC: 1838 AN: 2592

European-Non Finnish (NFE) AF: 0.712 AC: 135855 AN: 190818

Other (OTH) AF: 0.718 AC: 12148 AN: 16926

GnomAD4 genome AF: 0.667 AC: 101359 AN: 151996 Hom.: 34281 Cov.: 31 AF XY: 0.662 AC XY: 49208 AN XY: 74282

African (AFR) AF: 0.576 AC: 23849 AN: 41428

American (AMR) AF: 0.606 AC: 9263 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2603 AN: 3470

East Asian (EAS) AF: 0.813 AC: 4208 AN: 5176

South Asian (SAS) AF: 0.813 AC: 3922 AN: 4822

European-Finnish (FIN) AF: 0.588 AC: 6206 AN: 10548

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

European-Non Finnish (NFE) AF: 0.720 AC: 48939 AN: 67964

Other (OTH) AF: 0.685 AC: 1441 AN: 2104

Alfa AF: 0.697 Hom.: 88450

Bravo AF: 0.659

Asia WGS AF: 0.810 AC: 2817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	14
DANN	Benign	0.46
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; COSMIC: COSV72764368;