12-89753657-T-C

Position:

• chr12-89753657-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984543	XR_007063399.1	n.170+36294T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRPL2P1	ENST00000546688.1	n.745T>C		non_coding_transcript_exon_variant	1/1
	ENST00000651272.1	n.359+36294T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 0.561

Gnomad4 AMR exome AF: 0.551

Gnomad4 ASJ exome AF: 0.760

Gnomad4 EAS exome AF: 0.798

Gnomad4 SAS exome AF: 0.811

Gnomad4 FIN exome AF: 0.593

Gnomad4 NFE exome AF: 0.712

Gnomad4 OTH exome AF: 0.718

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

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.685

Alfa AF: 0.711 Hom.: 58946

Bravo AF: 0.659

Asia WGS AF: 0.810 AC: 2817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	14
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10858925; hg19: chr12-90147434; COSMIC: COSV72764368;