Variant chr5-1801318-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000505818.1(MRPL36):c.-13+16T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 1,497,886 control chromosomes in the GnomAD database, including 547,640 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.74 ( 45242 hom., cov: 37)

Exomes 𝑓: 0.86 ( 502398 hom. )

Consequence

MRPL36
ENST00000505818.1 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.904

Variant links:

Genes affected

MRPL36 (HGNC:14490): (mitochondrial ribosomal protein L36) 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. A pseudogene corresponding to this gene is found on chromosome 2p. [provided by RefSeq, Jul 2008]

MRPL36 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BP6

Variant 5-1801318-A-G is Benign according to our data. Variant chr5-1801318-A-G is described in ClinVar as [Benign]. Clinvar id is 1253294.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MRPL36	XM_011514080.3 linkuse as main transcript	c.33+16T>C		intron_variant
MRPL36	XM_017009751.3 linkuse as main transcript			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MRPL36	ENST00000505818.1 linkuse as main transcript	c.-13+16T>C		intron_variant		3		P1

Frequencies

GnomAD3 genomes

AF:

0.744

AC:

112810

AN:

151598

Hom.:

45235

Cov.:

show subpopulations

Gnomad AFR

AF:

0.437

Gnomad AMI

AF:

0.945

Gnomad AMR

AF:

0.844

Gnomad ASJ

AF:

0.848

Gnomad EAS

AF:

0.451

Gnomad SAS

AF:

0.729

Gnomad FIN

AF:

0.918

Gnomad MID

AF:

0.794

Gnomad NFE

AF:

0.895

Gnomad OTH

AF:

0.783

GnomAD4 exome

AF:

0.857

AC:

1154278

AN:

1346170

Hom.:

502398

Cov.:

AF XY:

0.856

AC XY:

563178

AN XY:

658300

show subpopulations

Gnomad4 AFR exome

AF:

0.420

Gnomad4 AMR exome

AF:

0.863

Gnomad4 ASJ exome

AF:

0.846

Gnomad4 EAS exome

AF:

0.484

Gnomad4 SAS exome

AF:

0.741

Gnomad4 FIN exome

AF:

0.914

Gnomad4 NFE exome

AF:

0.892

Gnomad4 OTH exome

AF:

0.819

GnomAD4 genome

AF:

0.744

AC:

112843

AN:

151716

Hom.:

45242

Cov.:

AF XY:

0.744

AC XY:

55177

AN XY:

74150

show subpopulations

Gnomad4 AFR

AF:

0.437

Gnomad4 AMR

AF:

0.844

Gnomad4 ASJ

AF:

0.848

Gnomad4 EAS

AF:

0.450

Gnomad4 SAS

AF:

0.730

Gnomad4 FIN

AF:

0.918

Gnomad4 NFE

AF:

0.895

Gnomad4 OTH

AF:

0.781

Alfa

AF:

0.809

Hom.:

6592

Bravo

AF:

0.724

Asia WGS

AF:

0.602

AC:

2095

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 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.3

DANN

Benign

0.29

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