rs781364428
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000232.5(SGCB):c.23_24insAGCGGCGGCGGCGGC(p.Ala5_Ala9dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000664 in 150,690 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. A8A) has been classified as Likely benign.
Frequency
Consequence
NM_000232.5 inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SGCB | NM_000232.5 | c.23_24insAGCGGCGGCGGCGGC | p.Ala5_Ala9dup | inframe_insertion | 1/6 | ENST00000381431.10 | |
SGCB | XM_047416074.1 | c.23_24insAGCGGCGGCGGCGGC | p.Ala5_Ala9dup | inframe_insertion | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGCB | ENST00000381431.10 | c.23_24insAGCGGCGGCGGCGGC | p.Ala5_Ala9dup | inframe_insertion | 1/6 | 1 | NM_000232.5 | P1 | |
SGCB | ENST00000506357.5 | c.9_10insAGCGGCGGCGGCGGC | p.Ala5_Glu6insAlaAlaAlaAlaAla | inframe_insertion, NMD_transcript_variant | 1/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000664 AC: 1AN: 150690Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000440 AC: 5AN: 1135466Hom.: 0 Cov.: 31 AF XY: 0.00000547 AC XY: 3AN XY: 548178
GnomAD4 genome ? AF: 0.00000664 AC: 1AN: 150690Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73560
ClinVar
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2E Uncertain:3
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 29, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Feb 09, 2022 | This variant, c.9_23dup, results in the insertion of 5 amino acid(s) of the SGCB protein (p.Ala5_Ala9dup), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SGCB-related conditions. ClinVar contains an entry for this variant (Variation ID: 551330). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Apr 04, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at