rs104893869
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_000232.5(SGCB):c.272G>T(p.Arg91Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,488 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R91P) has been classified as Pathogenic.
Frequency
Consequence
NM_000232.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SGCB | NM_000232.5 | c.272G>T | p.Arg91Leu | missense_variant | 3/6 | ENST00000381431.10 | |
SGCB | XM_047416074.1 | c.62G>T | p.Arg21Leu | missense_variant | 2/5 | ||
SGCB | XM_047416075.1 | c.-26G>T | 5_prime_UTR_variant | 2/5 | |||
SGCB | XM_047416076.1 | c.-26G>T | 5_prime_UTR_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGCB | ENST00000381431.10 | c.272G>T | p.Arg91Leu | missense_variant | 3/6 | 1 | NM_000232.5 | P1 | |
SGCB | ENST00000506357.5 | c.*54G>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/5 | 5 | ||||
SGCB | ENST00000514133.1 | c.*67G>T | 3_prime_UTR_variant, NMD_transcript_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251460Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135902
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461488Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727070
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2E Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 1998 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Aug 01, 2019 | - - |
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 20, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at