Variant chr3-131468063-GA-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_007208.4(MRPL3):c.894+27del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 1,136,162 control chromosomes in the GnomAD database, including 10,040 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 1344 hom., cov: 29)

Exomes 𝑓: 0.15 ( 8696 hom. )

Consequence

MRPL3
NM_007208.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.70

Variant links:

Genes affected

MRPL3 (HGNC:10379): (mitochondrial ribosomal protein L3) 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 that belongs to the L3P ribosomal protein family. A pseudogene corresponding to this gene is found on chromosome 13q. [provided by RefSeq, Jul 2008]

MRPL3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 3-131468063-GA-G is Benign according to our data. Variant chr3-131468063-GA-G is described in ClinVar as [Benign]. Clinvar id is 1292149.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-131468063-GA-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MRPL3	NM_007208.4 linkuse as main transcript	c.894+27del		intron_variant		ENST00000264995.8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
MRPL3	ENST00000264995.8 linkuse as main transcript	c.894+27del	intron_variant	1	NM_007208.4	P1
MRPL3	ENST00000425847.6 linkuse as main transcript	c.975+27del	intron_variant	2
MRPL3	ENST00000511168.5 linkuse as main transcript	c.937+27del	intron_variant	2
MRPL3	ENST00000510043.1 linkuse as main transcript	n.318+27del	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

17410

AN:

145422

Hom.:

1342

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0294

Gnomad AMI

AF:

0.161

Gnomad AMR

AF:

0.0820

Gnomad ASJ

AF:

0.253

Gnomad EAS

AF:

0.0652

Gnomad SAS

AF:

0.203

Gnomad FIN

AF:

0.167

Gnomad MID

AF:

0.195

Gnomad NFE

AF:

0.165

Gnomad OTH

AF:

0.123

GnomAD3 exomes

AF:

0.142

AC:

20961

AN:

147252

Hom.:

1036

AF XY:

0.149

AC XY:

12099

AN XY:

81446

show subpopulations

Gnomad AFR exome

AF:

0.0253

Gnomad AMR exome

AF:

0.0505

Gnomad ASJ exome

AF:

0.254

Gnomad EAS exome

AF:

0.0364

Gnomad SAS exome

AF:

0.192

Gnomad FIN exome

AF:

0.167

Gnomad NFE exome

AF:

0.162

Gnomad OTH exome

AF:

0.143

GnomAD4 exome

AF:

0.151

AC:

149891

AN:

990668

Hom.:

8696

Cov.:

AF XY:

0.153

AC XY:

76591

AN XY:

500828

show subpopulations

Gnomad4 AFR exome

AF:

0.0238

Gnomad4 AMR exome

AF:

0.0578

Gnomad4 ASJ exome

AF:

0.231

Gnomad4 EAS exome

AF:

0.0715

Gnomad4 SAS exome

AF:

0.184

Gnomad4 FIN exome

AF:

0.165

Gnomad4 NFE exome

AF:

0.156

Gnomad4 OTH exome

AF:

0.141

GnomAD4 genome

AF:

0.120

AC:

17412

AN:

145494

Hom.:

1344

Cov.:

AF XY:

0.121

AC XY:

8557

AN XY:

70780

show subpopulations

Gnomad4 AFR

AF:

0.0294

Gnomad4 AMR

AF:

0.0819

Gnomad4 ASJ

AF:

0.253

Gnomad4 EAS

AF:

0.0654

Gnomad4 SAS

AF:

0.203

Gnomad4 FIN

AF:

0.167

Gnomad4 NFE

AF:

0.165

Gnomad4 OTH

AF:

0.126

Bravo

AF:

0.102

Asia WGS

AF:

0.135

AC:

466

AN:

3450

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

Aug 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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