chr4-52029884-A-G
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
Consequence
NM_000232.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SGCB | NM_000232.5 | c.244-21T>C | intron_variant | Intron 2 of 5 | ENST00000381431.10 | NP_000223.1 | ||
SGCB | XM_047416074.1 | c.34-21T>C | intron_variant | Intron 1 of 4 | XP_047272030.1 | |||
SGCB | XM_047416075.1 | c.-54-21T>C | intron_variant | Intron 1 of 4 | XP_047272031.1 | |||
SGCB | XM_047416076.1 | c.-54-21T>C | intron_variant | Intron 1 of 4 | XP_047272032.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SGCB | ENST00000381431.10 | c.244-21T>C | intron_variant | Intron 2 of 5 | 1 | NM_000232.5 | ENSP00000370839.6 | |||
SGCB | ENST00000506357.5 | n.*26-21T>C | intron_variant | Intron 3 of 4 | 5 | ENSP00000421235.1 | ||||
SGCB | ENST00000514133.1 | n.*39-21T>C | intron_variant | Intron 2 of 3 | 5 | ENSP00000425818.1 |
Frequencies
GnomAD3 genomes AF: 0.437 AC: 66430AN: 151900Hom.: 17068 Cov.: 32
GnomAD3 exomes AF: 0.499 AC: 124938AN: 250610Hom.: 33187 AF XY: 0.497 AC XY: 67273AN XY: 135458
GnomAD4 exome AF: 0.534 AC: 767583AN: 1437600Hom.: 211123 Cov.: 26 AF XY: 0.530 AC XY: 379826AN XY: 716764
GnomAD4 genome AF: 0.437 AC: 66474AN: 152016Hom.: 17075 Cov.: 32 AF XY: 0.431 AC XY: 31999AN XY: 74268
ClinVar
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2E Benign:3
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not provided Benign:2
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. -
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not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at