rs882968

Positions:

• chr12-89753487-C-A
• chr12-89753487-C-G
• chr12-89753487-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.54).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984543	XR_007063399.1	n.170+36124C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MRPL2P1	ENST00000546688.1	n.575C>A		non_coding_transcript_exon_variant	1/1
	ENST00000651272.1	n.359+36124C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 0.506

Gnomad4 AMR exome AF: 0.541

Gnomad4 ASJ exome AF: 0.736

Gnomad4 EAS exome AF: 0.778

Gnomad4 SAS exome AF: 0.805

Gnomad4 FIN exome AF: 0.587

Gnomad4 NFE exome AF: 0.639

Gnomad4 OTH exome AF: 0.676

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

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.751

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.685

Alfa AF: 0.575 Hom.: 1526

Bravo AF: 0.666

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	13
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs882968; hg19: chr12-90147264; COSMIC: COSV72764355;