rs73151675
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_016038.4(SBDS):c.651C>T(p.Phe217=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0491 in 1,613,608 control chromosomes in the GnomAD database, including 2,252 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.036 ( 136 hom., cov: 32)
Exomes 𝑓: 0.050 ( 2116 hom. )
Consequence
SBDS
NM_016038.4 synonymous
NM_016038.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 5.24
Genes affected
SBDS (HGNC:19440): (SBDS ribosome maturation factor) This gene encodes a highly conserved protein that plays an essential role in ribosome biogenesis. The encoded protein interacts with elongation factor-like GTPase 1 to disassociate eukaryotic initiation factor 6 from the late cytoplasmic pre-60S ribosomal subunit allowing assembly of the 80S subunit. Mutations within this gene are associated with the autosomal recessive disorder Shwachman-Bodian-Diamond syndrome. This gene has a closely linked pseudogene that is distally located. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 7-66988473-G-A is Benign according to our data. Variant chr7-66988473-G-A is described in ClinVar as [Benign]. Clinvar id is 21544.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0525 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SBDS | NM_016038.4 | c.651C>T | p.Phe217= | synonymous_variant | 5/5 | ENST00000246868.7 | NP_057122.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SBDS | ENST00000246868.7 | c.651C>T | p.Phe217= | synonymous_variant | 5/5 | 1 | NM_016038.4 | ENSP00000246868 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0359 AC: 5452AN: 152036Hom.: 136 Cov.: 32
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GnomAD3 exomes AF: 0.0386 AC: 9710AN: 251264Hom.: 273 AF XY: 0.0390 AC XY: 5300AN XY: 135836
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GnomAD4 exome AF: 0.0505 AC: 73765AN: 1461454Hom.: 2116 Cov.: 31 AF XY: 0.0498 AC XY: 36211AN XY: 727054
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GnomAD4 genome AF: 0.0358 AC: 5452AN: 152154Hom.: 136 Cov.: 32 AF XY: 0.0342 AC XY: 2541AN XY: 74382
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ClinVar
Significance: Benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Mar 29, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 09, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Shwachman-Diamond syndrome 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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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