17-8377741-A-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000987.5(RPL26):c.310-49T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00309 in 1,549,132 control chromosomes in the GnomAD database, including 157 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0035 ( 12 hom., cov: 33)
Exomes 𝑓: 0.0030 ( 145 hom. )
Consequence
RPL26
NM_000987.5 intron
NM_000987.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.592
Genes affected
RPL26 (HGNC:10327): (ribosomal protein L26) 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 L24P family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Mutations in this gene result in Diamond-Blackfan anemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]
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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=-0.8).
BP6
?
Variant 17-8377741-A-C is Benign according to our data. Variant chr17-8377741-A-C is described in ClinVar as [Benign]. Clinvar id is 1277419.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0543 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPL26 | NM_000987.5 | c.310-49T>G | intron_variant | ENST00000648839.1 | |||
RPL26 | NM_001315530.2 | c.310-49T>G | intron_variant | ||||
RPL26 | NM_001315531.2 | c.310-49T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL26 | ENST00000648839.1 | c.310-49T>G | intron_variant | NM_000987.5 | P1 | ||||
ENST00000666354.1 | n.154-3304A>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00354 AC: 538AN: 152184Hom.: 12 Cov.: 33
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GnomAD3 exomes AF: 0.0107 AC: 2393AN: 223090Hom.: 77 AF XY: 0.00836 AC XY: 1021AN XY: 122172
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GnomAD4 exome AF: 0.00305 AC: 4254AN: 1396830Hom.: 145 Cov.: 24 AF XY: 0.00278 AC XY: 1927AN XY: 692448
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GnomAD4 genome ? AF: 0.00353 AC: 537AN: 152302Hom.: 12 Cov.: 33 AF XY: 0.00393 AC XY: 293AN XY: 74482
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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 | GeneDx | Oct 21, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at