chr3-40462029-A-ACTGCTGCTGCTGCTGCTG
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP3BP6_ModerateBA1
The NM_001034996.3(RPL14):c.460_477dup(p.Ala154_Ala159dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.052 ( 240 hom., cov: 0)
Exomes 𝑓: 0.056 ( 2527 hom. )
Failed GnomAD Quality Control
Consequence
RPL14
NM_001034996.3 inframe_insertion
NM_001034996.3 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.00
Genes affected
RPL14 (HGNC:10305): (ribosomal protein L14) 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 L14E family of ribosomal proteins. It contains a basic region-leucine zipper (bZIP)-like domain. The protein is located in the cytoplasm. This gene contains a trinucleotide (GCT) repeat tract whose length is highly polymorphic; these triplet repeats result in a stretch of alanine residues in the encoded protein. Transcript variants utilizing alternative polyA signals and alternative 5'-terminal exons exist but all 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 Benign. Variant got -11 ACMG points.
BP3
?
Nonframeshift variant in repetitive region in NM_001034996.3
BP6
?
Variant 3-40462029-A-ACTGCTGCTGCTGCTGCTG is Benign according to our data. Variant chr3-40462029-A-ACTGCTGCTGCTGCTGCTG is described in ClinVar as [Benign]. Clinvar id is 770140.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0658 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPL14 | NM_001034996.3 | c.460_477dup | p.Ala154_Ala159dup | inframe_insertion | 6/6 | ENST00000396203.7 | |
RPL14 | NM_003973.5 | c.460_477dup | p.Ala154_Ala159dup | inframe_insertion | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL14 | ENST00000396203.7 | c.460_477dup | p.Ala154_Ala159dup | inframe_insertion | 6/6 | 1 | NM_001034996.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0519 AC: 7690AN: 148278Hom.: 241 Cov.: 0
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0563 AC: 78809AN: 1398724Hom.: 2527 Cov.: 80 AF XY: 0.0561 AC XY: 38942AN XY: 694454
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GnomAD4 genome ? AF: 0.0518 AC: 7685AN: 148386Hom.: 240 Cov.: 0 AF XY: 0.0498 AC XY: 3600AN XY: 72280
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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 | Invitae | Dec 31, 2019 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at