Variant rs882968 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.44

Variant links:

Genes affected

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

MRPL2P1 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

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	Protein	UniProt
LOC107984543	XR_007063399.1 linkuse as main transcript	n.170+36124C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.667

AC:

101266

AN:

151840

Hom.:

34247

Cov.:

show subpopulations

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.:

AF XY:

0.671

AC XY:

145752

AN XY:

217148

show subpopulations

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.:

AF XY:

0.662

AC XY:

49189

AN XY:

74256

show subpopulations

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

DANN

Benign

0.71

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over