Variant 8-80030026-C-CGGGCTCCACCTTCTGTAGGGGCTCCACCTTCTGTAGGGGCTCCACCTTCTGTAG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The ENST00000276585.9(MRPS28):c.213+9_213+10insCTACAGAAGGTGGAGCCCCTACAGAAGGTGGAGCCCCTACAGAAGGTGGAGCCC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0024 ( 7 hom., cov: 32)

Exomes 𝑓: 0.000097 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

MRPS28
ENST00000276585.9 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.75

Variant links:

Genes affected

MRPS28 (HGNC:14513): (mitochondrial ribosomal protein S28) 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 28S subunit protein that has been called mitochondrial ribosomal protein S35 in the literature. [provided by RefSeq, Jul 2008]

MRPS28 links:

TPD52-MRPS28 (HGNC:):

TPD52-MRPS28 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP6

Variant 8-80030026-C-CGGGCTCCACCTTCTGTAGGGGCTCCACCTTCTGTAGGGGCTCCACCTTCTGTAG is Benign according to our data. Variant chr8-80030026-C-CGGGCTCCACCTTCTGTAGGGGCTCCACCTTCTGTAGGGGCTCCACCTTCTGTAG is described in ClinVar as [Likely_benign]. Clinvar id is 2673154.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MRPS28	NM_014018.3 linkuse as main transcript	c.213+9_213+10insCTACAGAAGGTGGAGCCCCTACAGAAGGTGGAGCCCCTACAGAAGGTGGAGCCC		intron_variant		ENST00000276585.9	NP_054737.1
TPD52-MRPS28	NM_001387778.1 linkuse as main transcript	c.435+12593_435+12594insCTACAGAAGGTGGAGCCCCTACAGAAGGTGGAGCCCCTACAGAAGGTGGAGCCC		intron_variant			NP_001374707.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
MRPS28	ENST00000276585.9 linkuse as main transcript	c.213+9_213+10insCTACAGAAGGTGGAGCCCCTACAGAAGGTGGAGCCCCTACAGAAGGTGGAGCCC	intron_variant	1	NM_014018.3	ENSP00000276585	P1
MRPS28	ENST00000518271.1 linkuse as main transcript	c.179+27_179+28insCTACAGAAGGTGGAGCCCCTACAGAAGGTGGAGCCCCTACAGAAGGTGGAGCCC	intron_variant	5		ENSP00000427846
MRPS28	ENST00000521605.1 linkuse as main transcript	c.213+9_213+10insCTACAGAAGGTGGAGCCCCTACAGAAGGTGGAGCCCCTACAGAAGGTGGAGCCC	intron_variant	2		ENSP00000427965
MRPS28	ENST00000522987.1 linkuse as main transcript	n.201+27_201+28insCTACAGAAGGTGGAGCCCCTACAGAAGGTGGAGCCCCTACAGAAGGTGGAGCCC	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

365

AN:

151766

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00865

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000458

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.000958

GnomAD3 exomes

AF:

0.000328

AC:

AN:

246720

Hom.:

AF XY:

0.000210

AC XY:

AN XY:

133598

show subpopulations

Gnomad AFR exome

AF:

0.00495

Gnomad AMR exome

AF:

0.0000875

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000897

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000974

AC:

142

AN:

1458110

Hom.:

Cov.:

AF XY:

0.0000965

AC XY:

AN XY:

725146

show subpopulations

Gnomad4 AFR exome

AF:

0.00365

Gnomad4 AMR exome

AF:

0.000112

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000116

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000450

Gnomad4 OTH exome

AF:

0.000199

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00241

AC:

366

AN:

151884

Hom.:

Cov.:

AF XY:

0.00211

AC XY:

157

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.00865

Gnomad4 AMR

AF:

0.000458

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000147

Gnomad4 OTH

AF:

0.000948

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2023

MRPS28: BS2 -

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

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over