Variant chr11-68903812-G-GCCGCCGCCATCTTC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000362034.7(MRPL21):c.-3_-2insGAAGATGGCGGCGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 1,611,806 control chromosomes in the GnomAD database, including 80,201 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.32 ( 8329 hom., cov: 0)

Exomes 𝑓: 0.31 ( 71872 hom. )

Consequence

MRPL21
ENST00000362034.7 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0570

Variant links:

Genes affected

MRPL21 (HGNC:14479): (mitochondrial ribosomal protein L21) Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 39S subunit protein. Multiple transcript variants encoding different isoforms were identified through sequence analysis although some may be subject to nonsense-mediated decay (NMD). [provided by RefSeq, Jul 2008]

MRPL21 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 11-68903812-G-GCCGCCGCCATCTTC is Benign according to our data. Variant chr11-68903812-G-GCCGCCGCCATCTTC is described in ClinVar as [Benign]. Clinvar id is 1245933.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
MRPL21	NM_181514.2 linkuse as main transcript	c.-3_-2insGAAGATGGCGGCGG	5_prime_UTR_variant	1/7	ENST00000362034.7	NP_852615.1
MRPL21	NM_181515.2 linkuse as main transcript	c.-271_-270insGAAGATGGCGGCGG	5_prime_UTR_variant	1/7		NP_852616.1
MRPL21	XM_005273823.5 linkuse as main transcript	c.-3_-2insGAAGATGGCGGCGG	5_prime_UTR_variant	1/6		XP_005273880.1
MRPL21	XR_247190.5 linkuse as main transcript	n.20_21insGAAGATGGCGGCGG	non_coding_transcript_exon_variant	1/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRPL21	ENST00000362034.7 linkuse as main transcript	c.-3_-2insGAAGATGGCGGCGG		5_prime_UTR_variant	1/7	1	NM_181514.2	ENSP00000354580	P1	Q7Z2W9-1

Frequencies

GnomAD3 genomes

AF:

0.322

AC:

49006

AN:

152004

Hom.:

8322

Cov.:

show subpopulations

Gnomad AFR

AF:

0.388

Gnomad AMI

AF:

0.152

Gnomad AMR

AF:

0.201

Gnomad ASJ

AF:

0.368

Gnomad EAS

AF:

0.215

Gnomad SAS

AF:

0.485

Gnomad FIN

AF:

0.366

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.301

Gnomad OTH

AF:

0.288

GnomAD4 exome

AF:

0.306

AC:

447229

AN:

1459682

Hom.:

71872

Cov.:

AF XY:

0.314

AC XY:

227789

AN XY:

726076

show subpopulations

Gnomad4 AFR exome

AF:

0.395

Gnomad4 AMR exome

AF:

0.142

Gnomad4 ASJ exome

AF:

0.357

Gnomad4 EAS exome

AF:

0.246

Gnomad4 SAS exome

AF:

0.490

Gnomad4 FIN exome

AF:

0.376

Gnomad4 NFE exome

AF:

0.293

Gnomad4 OTH exome

AF:

0.311

GnomAD4 genome

AF:

0.322

AC:

49049

AN:

152124

Hom.:

8329

Cov.:

AF XY:

0.327

AC XY:

24304

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.388

Gnomad4 AMR

AF:

0.201

Gnomad4 ASJ

AF:

0.368

Gnomad4 EAS

AF:

0.215

Gnomad4 SAS

AF:

0.485

Gnomad4 FIN

AF:

0.366

Gnomad4 NFE

AF:

0.300

Gnomad4 OTH

AF:

0.287

Alfa

AF:

0.239

Hom.:

742

Asia WGS

AF:

0.353

AC:

1226

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 16, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over