Variant chr3-131468049-CA-C 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+41del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.66 ( 29785 hom., cov: 0)

Exomes 𝑓: 0.47 ( 27967 hom. )

Failed GnomAD Quality Control

Consequence

MRPL3
NM_007208.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.292

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 3-131468049-CA-C is Benign according to our data. Variant chr3-131468049-CA-C is described in ClinVar as [Benign]. Clinvar id is 1239761.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 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+41del		intron_variant		ENST00000264995.8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
MRPL3	ENST00000264995.8 linkuse as main transcript	c.894+41del	intron_variant	1	NM_007208.4	P1
MRPL3	ENST00000425847.6 linkuse as main transcript	c.975+41del	intron_variant	2
MRPL3	ENST00000511168.5 linkuse as main transcript	c.937+41del	intron_variant	2
MRPL3	ENST00000510043.1 linkuse as main transcript	n.318+41del	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.658

AC:

90613

AN:

137620

Hom.:

29757

Cov.:

show subpopulations

Gnomad AFR

AF:

0.875

Gnomad AMI

AF:

0.597

Gnomad AMR

AF:

0.599

Gnomad ASJ

AF:

0.555

Gnomad EAS

AF:

0.448

Gnomad SAS

AF:

0.492

Gnomad FIN

AF:

0.547

Gnomad MID

AF:

0.659

Gnomad NFE

AF:

0.583

Gnomad OTH

AF:

0.653

GnomAD3 exomes

AF:

0.516

AC:

58001

AN:

112418

Hom.:

5694

AF XY:

0.509

AC XY:

31626

AN XY:

62146

show subpopulations

Gnomad AFR exome

AF:

0.692

Gnomad AMR exome

AF:

0.506

Gnomad ASJ exome

AF:

0.481

Gnomad EAS exome

AF:

0.496

Gnomad SAS exome

AF:

0.483

Gnomad FIN exome

AF:

0.495

Gnomad NFE exome

AF:

0.514

Gnomad OTH exome

AF:

0.517

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.471

AC:

328236

AN:

697542

Hom.:

27967

Cov.:

AF XY:

0.472

AC XY:

169258

AN XY:

358756

show subpopulations

Gnomad4 AFR exome

AF:

0.615

Gnomad4 AMR exome

AF:

0.480

Gnomad4 ASJ exome

AF:

0.457

Gnomad4 EAS exome

AF:

0.459

Gnomad4 SAS exome

AF:

0.442

Gnomad4 FIN exome

AF:

0.485

Gnomad4 NFE exome

AF:

0.468

Gnomad4 OTH exome

AF:

0.475

GnomAD4 genome

AF:

0.659

AC:

90662

AN:

137662

Hom.:

29785

Cov.:

AF XY:

0.653

AC XY:

43493

AN XY:

66648

show subpopulations

Gnomad4 AFR

AF:

0.875

Gnomad4 AMR

AF:

0.599

Gnomad4 ASJ

AF:

0.555

Gnomad4 EAS

AF:

0.447

Gnomad4 SAS

AF:

0.493

Gnomad4 FIN

AF:

0.547

Gnomad4 NFE

AF:

0.583

Gnomad4 OTH

AF:

0.652

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