17-8377707-G-GA
Position:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_000987.5(RPL26):c.310-16_310-15insT variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000578 in 1,591,592 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★). There are indicators that this mutation may affect the branch point..
Frequency
Genomes: 𝑓 0.00030 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000033 ( 0 hom. )
Consequence
RPL26
NM_000987.5 splice_polypyrimidine_tract, intron
NM_000987.5 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.560
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 17-8377707-G-GA is Benign according to our data. Variant chr17-8377707-G-GA is described in ClinVar as [Benign]. Clinvar id is 2157610.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd4 at 45 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPL26 | NM_000987.5 | c.310-16_310-15insT | splice_polypyrimidine_tract_variant, intron_variant | ENST00000648839.1 | |||
RPL26 | NM_001315530.2 | c.310-16_310-15insT | splice_polypyrimidine_tract_variant, intron_variant | ||||
RPL26 | NM_001315531.2 | c.310-16_310-15insT | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPL26 | ENST00000648839.1 | c.310-16_310-15insT | splice_polypyrimidine_tract_variant, intron_variant | NM_000987.5 | P1 | ||||
ENST00000666354.1 | n.154-3331dup | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000296 AC: 45AN: 151976Hom.: 0 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
45
AN:
151976
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000169 AC: 4AN: 236196Hom.: 0 AF XY: 0.0000233 AC XY: 3AN XY: 128578
GnomAD3 exomes
AF:
AC:
4
AN:
236196
Hom.:
AF XY:
AC XY:
3
AN XY:
128578
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000326 AC: 47AN: 1439616Hom.: 0 Cov.: 29 AF XY: 0.0000377 AC XY: 27AN XY: 715646
GnomAD4 exome
AF:
AC:
47
AN:
1439616
Hom.:
Cov.:
29
AF XY:
AC XY:
27
AN XY:
715646
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000296 AC: 45AN: 151976Hom.: 0 Cov.: 33 AF XY: 0.000350 AC XY: 26AN XY: 74232
GnomAD4 genome
?
AF:
AC:
45
AN:
151976
Hom.:
Cov.:
33
AF XY:
AC XY:
26
AN XY:
74232
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Diamond-Blackfan anemia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 11, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BranchPoint Hunter
?
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at