10-110567823-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP2PP3
The NM_005445.4(SMC3):āc.7A>Gā(p.Ile3Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,192 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 Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I3R) has been classified as Uncertain significance.
Frequency
Consequence
NM_005445.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMC3 | NM_005445.4 | c.7A>G | p.Ile3Val | missense_variant | 1/29 | ENST00000361804.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMC3 | ENST00000361804.5 | c.7A>G | p.Ile3Val | missense_variant | 1/29 | 1 | NM_005445.4 | P1 | |
SMC3 | ENST00000684988.1 | n.140A>G | non_coding_transcript_exon_variant | 1/25 | |||||
SMC3 | ENST00000691297.1 | n.140A>G | non_coding_transcript_exon_variant | 1/17 | |||||
SMC3 | ENST00000691527.1 | n.97A>G | non_coding_transcript_exon_variant | 1/16 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461192Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726938
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Cornelia de Lange syndrome 3 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Aug 12, 2019 | This variant was classified as: Uncertain significance. The available evidence on this variant's pathogenicity is insufficient or conflicting. The following ACMG criteria were applied in classifying this variant: PM2,PP2,PP3. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at