rs882968

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRPL2P1		n.89753487C>A		intragenic_variant
LOC107984543	XR_007063399.1	n.170+36124C>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRPL2P1	ENST00000546688.1	n.575C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ATP2B1-AS1	ENST00000651272.1	n.359+36124C>A		intron_variant	Intron 2 of 6
ENSG00000296746	ENST00000741520.1	n.176-15050G>T		intron_variant	Intron 1 of 3

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 v4.3

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;