chr19-5678617-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_205767.3(MICOS13):c.291G>A(p.Val97=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000143 in 1,393,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
MICOS13
NM_205767.3 synonymous
NM_205767.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.13
Genes affected
MICOS13 (HGNC:33702): (mitochondrial contact site and cristae organizing system subunit 13) Involved in cristae formation. Located in mitochondrial crista junction and nucleoplasm. Part of MICOS complex. Implicated in combined oxidative phosphorylation deficiency 37. [provided by Alliance of Genome Resources, Apr 2022]
RPL36 (HGNC:13631): (ribosomal protein L36) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L36E family of ribosomal proteins. It is located in the cytoplasm. Transcript variants derived from alternative splicing exist; they encode the same protein. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 19-5678617-C-T is Benign according to our data. Variant chr19-5678617-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2171050.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.13 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MICOS13 | NM_205767.3 | c.291G>A | p.Val97= | synonymous_variant | 4/4 | ENST00000309324.9 | |
MICOS13 | NM_001308240.2 | c.357G>A | p.Val119= | synonymous_variant | 5/5 | ||
MICOS13 | NM_001365761.2 | c.357G>A | p.Val119= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MICOS13 | ENST00000309324.9 | c.291G>A | p.Val97= | synonymous_variant | 4/4 | 1 | NM_205767.3 | P1 | |
MICOS13 | ENST00000587950.5 | c.357G>A | p.Val119= | synonymous_variant | 4/4 | 2 | |||
RPL36 | ENST00000579649.5 | c.-60+3645C>T | intron_variant | 5 | P1 | ||||
MICOS13 | ENST00000585605.1 | n.390G>A | non_coding_transcript_exon_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00000669 AC: 1AN: 149420Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 78934
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GnomAD4 exome AF: 0.00000143 AC: 2AN: 1393742Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 687456
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 28, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at