rs1553940660
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_000232.5(SGCB):c.243+3_243+6del variant causes a splice donor 5th base, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000014 in 1,425,326 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000232.5 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SGCB | NM_000232.5 | c.243+3_243+6del | splice_donor_5th_base_variant, intron_variant | ENST00000381431.10 | |||
SGCB | XM_047416074.1 | c.34-3565_34-3562del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGCB | ENST00000381431.10 | c.243+3_243+6del | splice_donor_5th_base_variant, intron_variant | 1 | NM_000232.5 | P1 | |||
SGCB | ENST00000506357.5 | c.229+3_229+6del | splice_donor_5th_base_variant, intron_variant, NMD_transcript_variant | 5 | |||||
SGCB | ENST00000514133.1 | c.210+3_210+6del | splice_donor_5th_base_variant, intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000140 AC: 2AN: 1425326Hom.: 0 AF XY: 0.00000281 AC XY: 2AN XY: 711598
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2E Pathogenic:2Uncertain:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Jul 10, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Nov 07, 2017 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 2000 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at