chr5-1801313-C-CG

Position:

• chr5-1801313-C-CG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000505818.1(MRPL36):​c.-13+20_-13+21insC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 1,479,734 control chromosomes in the GnomAD database, including 540,383 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.74 (45200 hom., cov: 0)
  • Exomes 𝑓: 0.86 (495183 hom.)
• Consequence: MRPL36 ENST00000505818.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0150

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 5-1801313-C-CG is Benign according to our data. Variant chr5-1801313-C-CG is described in ClinVar as [Benign]. Clinvar id is 1266183.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MRPL36	XM_011514080.3	c.33+20_33+21insC		intron_variant
MRPL36	XM_017009751.3			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MRPL36	ENST00000505818.1	c.-13+20_-13+21insC		intron_variant		3		P1

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112743 AN: 151596 Hom.: 45195 Cov.: 0

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.784

GnomAD4 exome AF: 0.857 AC: 1138047 AN: 1328022 Hom.: 495183 Cov.: 27 AF XY: 0.855 AC XY: 553790 AN XY: 647774

Gnomad4 AFR exome AF: 0.418

Gnomad4 AMR exome AF: 0.861

Gnomad4 ASJ exome AF: 0.844

Gnomad4 EAS exome AF: 0.479

Gnomad4 SAS exome AF: 0.739

Gnomad4 FIN exome AF: 0.913

Gnomad4 NFE exome AF: 0.891

Gnomad4 OTH exome AF: 0.818

GnomAD4 genome AF: 0.743 AC: 112773 AN: 151712 Hom.: 45200 Cov.: 0 AF XY: 0.744 AC XY: 55121 AN XY: 74130

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.844

Gnomad4 ASJ AF: 0.847

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.782

Alfa AF: 0.743 Hom.: 1928

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34372448; hg19: chr5-1801427; COSMIC: COSV56876338; COSMIC: COSV56876338;