Variant 5-44809331-G-GGAGCCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP3BP6_ModerateBS1BS2

The NM_016640.4(MRPS30):c.384_389dup(p.Glu134_Pro135dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00707 in 1,610,934 control chromosomes in the GnomAD database, including 84 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0041 ( 6 hom., cov: 33)

Exomes 𝑓: 0.0074 ( 78 hom. )

Consequence

MRPS30
NM_016640.4 inframe_insertion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.160

Variant links:

Genes affected

MRPS30 (HGNC:8769): (mitochondrial ribosomal protein S30) 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 is similar to the chicken pro-apoptotic protein p52. Transcript variants using alternative promoters or polyA sites have been mentioned in the literature but the complete description of these sequences is not available. [provided by RefSeq, Jul 2008]

MRPS30 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_016640.4

BP6

Variant 5-44809331-G-GGAGCCC is Benign according to our data. Variant chr5-44809331-G-GGAGCCC is described in ClinVar as [Likely_benign]. Clinvar id is 2655453.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00738 (10770/1458626) while in subpopulation MID AF= 0.0239 (138/5764). AF 95% confidence interval is 0.0207. There are 78 homozygotes in gnomad4_exome. There are 5350 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MRPS30	NM_016640.4 linkuse as main transcript	c.384_389dup	p.Glu134_Pro135dup	inframe_insertion	1/5	ENST00000507110.6	NP_057724.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRPS30	ENST00000507110.6 linkuse as main transcript	c.384_389dup	p.Glu134_Pro135dup	inframe_insertion	1/5	1	NM_016640.4	ENSP00000424328	P1

Frequencies

GnomAD3 genomes

AF:

0.00410

AC:

624

AN:

152190

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00135

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.00242

Gnomad ASJ

AF:

0.0132

Gnomad EAS

AF:

0.00155

Gnomad SAS

AF:

0.00663

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00606

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00476

AC:

1153

AN:

242108

Hom.:

AF XY:

0.00512

AC XY:

675

AN XY:

131818

show subpopulations

Gnomad AFR exome

AF:

0.00107

Gnomad AMR exome

AF:

0.00209

Gnomad ASJ exome

AF:

0.0163

Gnomad EAS exome

AF:

0.000621

Gnomad SAS exome

AF:

0.00643

Gnomad FIN exome

AF:

0.000902

Gnomad NFE exome

AF:

0.00592

Gnomad OTH exome

AF:

0.00673

GnomAD4 exome

AF:

0.00738

AC:

10770

AN:

1458626

Hom.:

Cov.:

AF XY:

0.00737

AC XY:

5350

AN XY:

725480

show subpopulations

Gnomad4 AFR exome

AF:

0.00153

Gnomad4 AMR exome

AF:

0.00232

Gnomad4 ASJ exome

AF:

0.0185

Gnomad4 EAS exome

AF:

0.00162

Gnomad4 SAS exome

AF:

0.00596

Gnomad4 FIN exome

AF:

0.00103

Gnomad4 NFE exome

AF:

0.00810

Gnomad4 OTH exome

AF:

0.00607

GnomAD4 genome

AF:

0.00410

AC:

624

AN:

152308

Hom.:

Cov.:

AF XY:

0.00377

AC XY:

281

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.00135

Gnomad4 AMR

AF:

0.00242

Gnomad4 ASJ

AF:

0.0132

Gnomad4 EAS

AF:

0.00155

Gnomad4 SAS

AF:

0.00663

Gnomad4 FIN

AF:

0.00132

Gnomad4 NFE

AF:

0.00606

Gnomad4 OTH

AF:

0.00378

Asia WGS

AF:

0.00231

AC:

AN:

3478

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

Feb 01, 2024

MRPS30: 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

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