3-131462637-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_007208.4(MRPL3):c.*86C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00136 in 1,287,404 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0068 ( 16 hom., cov: 32)
Exomes 𝑓: 0.00063 ( 4 hom. )
Consequence
MRPL3
NM_007208.4 3_prime_UTR
NM_007208.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0430
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]
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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=-0.85).
BP6
Variant 3-131462637-G-A is Benign according to our data. Variant chr3-131462637-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1193072.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00681 (1036/152238) while in subpopulation AFR AF= 0.0239 (991/41534). AF 95% confidence interval is 0.0226. There are 16 homozygotes in gnomad4. There are 509 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 16 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRPL3 | NM_007208.4 | c.*86C>T | 3_prime_UTR_variant | 10/10 | ENST00000264995.8 | NP_009139.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPL3 | ENST00000264995.8 | c.*86C>T | 3_prime_UTR_variant | 10/10 | 1 | NM_007208.4 | ENSP00000264995 | P1 | ||
MRPL3 | ENST00000425847.6 | c.*86C>T | 3_prime_UTR_variant | 11/11 | 2 | ENSP00000398536 | ||||
MRPL3 | ENST00000511168.5 | c.*86C>T | 3_prime_UTR_variant | 10/10 | 2 | ENSP00000424107 | ||||
MRPL3 | ENST00000510043.1 | n.557C>T | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00680 AC: 1035AN: 152120Hom.: 16 Cov.: 32
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GnomAD4 exome AF: 0.000630 AC: 715AN: 1135166Hom.: 4 Cov.: 14 AF XY: 0.000571 AC XY: 321AN XY: 562408
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GnomAD4 genome AF: 0.00681 AC: 1036AN: 152238Hom.: 16 Cov.: 32 AF XY: 0.00684 AC XY: 509AN XY: 74420
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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 | GeneDx | Jan 28, 2019 | - - |
Computational scores
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Benign
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DANN
Benign
RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at