chr5-1801063-G-T

Position:

• chr5-1801063-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000505818.1(MRPL36):​c.-13+271C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0632 in 152,324 control chromosomes in the GnomAD database, including 314 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.063 (314 hom., cov: 34)
• Consequence: MRPL36 ENST00000505818.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0780

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 5-1801063-G-T is Benign according to our data. Variant chr5-1801063-G-T is described in ClinVar as [Benign]. Clinvar id is 1278703.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.082 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MRPL36	XM_011514080.3	c.33+271C>A		intron_variant
MRPL36	XM_017009751.3	c.-13+175C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MRPL36	ENST00000505818.1	c.-13+271C>A		intron_variant		3		P1

Frequencies

GnomAD3 genomes AF: 0.0632 AC: 9620 AN: 152206 Hom.: 313 Cov.: 34

Gnomad AFR AF: 0.0842

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0548

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.0812

Gnomad SAS AF: 0.0275

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0599

Gnomad OTH AF: 0.0708

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0632 AC: 9633 AN: 152324 Hom.: 314 Cov.: 34 AF XY: 0.0608 AC XY: 4532 AN XY: 74492

Gnomad4 AFR AF: 0.0844

Gnomad4 AMR AF: 0.0546

Gnomad4 ASJ AF: 0.0622

Gnomad4 EAS AF: 0.0814

Gnomad4 SAS AF: 0.0279

Gnomad4 FIN AF: 0.0238

Gnomad4 NFE AF: 0.0599

Gnomad4 OTH AF: 0.0696

Alfa AF: 0.0601 Hom.: 85

Bravo AF: 0.0671

Asia WGS AF: 0.0640 AC: 221 AN: 3478

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 14, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs79824860; hg19: chr5-1801177;