rs225170
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000232.5(SGCB):c.244-21T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 1,589,616 control chromosomes in the GnomAD database, including 228,198 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.44 ( 17075 hom., cov: 32)
Exomes 𝑓: 0.53 ( 211123 hom. )
Consequence
SGCB
NM_000232.5 intron
NM_000232.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.452
Genes affected
SGCB (HGNC:10806): (sarcoglycan beta) This gene encodes a member of the sarcoglycan family. Sarcoglycans are transmembrane components in the dystrophin-glycoprotein complex which help stabilize the muscle fiber membranes and link the muscle cytoskeleton to the extracellular matrix. Mutations in this gene have been associated with limb-girdle muscular dystrophy.[provided by RefSeq, Oct 2008]
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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=-0.78).
BP6
Variant 4-52029884-A-G is Benign according to our data. Variant chr4-52029884-A-G is described in ClinVar as [Benign]. Clinvar id is 255605.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-52029884-A-G is described in Lovd as [Benign]. Variant chr4-52029884-A-G is described in Lovd as [Likely_benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SGCB | NM_000232.5 | c.244-21T>C | intron_variant | ENST00000381431.10 | NP_000223.1 | |||
SGCB | XM_047416074.1 | c.34-21T>C | intron_variant | XP_047272030.1 | ||||
SGCB | XM_047416075.1 | c.-54-21T>C | intron_variant | XP_047272031.1 | ||||
SGCB | XM_047416076.1 | c.-54-21T>C | intron_variant | XP_047272032.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SGCB | ENST00000381431.10 | c.244-21T>C | intron_variant | 1 | NM_000232.5 | ENSP00000370839 | P1 | |||
SGCB | ENST00000506357.5 | c.*26-21T>C | intron_variant, NMD_transcript_variant | 5 | ENSP00000421235 | |||||
SGCB | ENST00000514133.1 | c.*39-21T>C | intron_variant, NMD_transcript_variant | 5 | ENSP00000425818 |
Frequencies
GnomAD3 genomes AF: 0.437 AC: 66430AN: 151900Hom.: 17068 Cov.: 32
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GnomAD3 exomes AF: 0.499 AC: 124938AN: 250610Hom.: 33187 AF XY: 0.497 AC XY: 67273AN XY: 135458
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GnomAD4 exome AF: 0.534 AC: 767583AN: 1437600Hom.: 211123 Cov.: 26 AF XY: 0.530 AC XY: 379826AN XY: 716764
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GnomAD4 genome AF: 0.437 AC: 66474AN: 152016Hom.: 17075 Cov.: 32 AF XY: 0.431 AC XY: 31999AN XY: 74268
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ClinVar
Significance: Benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2E Benign:3
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 07, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Pars Genome Lab | Jun 15, 2021 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at