NM_000337.6:c.193-12G>T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_000337.6(SGCD):c.193-12G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000239 in 1,548,658 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000337.6 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SGCD | ENST00000337851.9 | c.193-12G>T | intron_variant | Intron 3 of 8 | 1 | NM_000337.6 | ENSP00000338343.4 | |||
SGCD | ENST00000435422.7 | c.190-12G>T | intron_variant | Intron 2 of 7 | 1 | ENSP00000403003.2 | ||||
SGCD | ENST00000517913.5 | c.193-12G>T | intron_variant | Intron 5 of 9 | 5 | ENSP00000429378.1 | ||||
SGCD | ENST00000524347.2 | n.*57-12G>T | intron_variant | Intron 4 of 5 | 5 | ENSP00000430794.1 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151836Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000812 AC: 2AN: 246406Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133584
GnomAD4 exome AF: 0.0000229 AC: 32AN: 1396712Hom.: 0 Cov.: 23 AF XY: 0.0000186 AC XY: 13AN XY: 698936
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151946Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74232
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign: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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The 193-12G>T variant in SGCD has not been previously reported in individuals wi th cardiomyopathy or in large population studies. This variant is located in the 3' splice region. Computational tools do not suggest an impact to splicing, tho ugh this information is not predictive enough to rule out pathogenicity. In summ ary, the clinical significance of the 193-12G>T variant is uncertain. -
Autosomal recessive limb-girdle muscular dystrophy type 2F;C1847667:Dilated cardiomyopathy 1L Uncertain:1
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Autosomal recessive limb-girdle muscular dystrophy type 2F Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at