chr9-104100147-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006444.3(SMC2):c.535A>G(p.Ile179Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000706 in 1,579,640 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006444.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMC2 | NM_006444.3 | c.535A>G | p.Ile179Val | missense_variant | 6/25 | ENST00000374793.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMC2 | ENST00000374793.8 | c.535A>G | p.Ile179Val | missense_variant | 6/25 | 1 | NM_006444.3 | P1 | |
SMC2 | ENST00000286398.11 | c.535A>G | p.Ile179Val | missense_variant | 6/25 | 1 | P1 | ||
SMC2 | ENST00000374787.7 | c.535A>G | p.Ile179Val | missense_variant | 6/25 | 2 | P1 | ||
SMC2 | ENST00000440179.5 | c.100A>G | p.Ile34Val | missense_variant | 4/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000493 AC: 75AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000563 AC: 123AN: 218524Hom.: 0 AF XY: 0.000587 AC XY: 70AN XY: 119316
GnomAD4 exome AF: 0.000729 AC: 1040AN: 1427434Hom.: 0 Cov.: 29 AF XY: 0.000709 AC XY: 503AN XY: 709938
GnomAD4 genome ? AF: 0.000493 AC: 75AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.000336 AC XY: 25AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.535A>G (p.I179V) alteration is located in exon 6 (coding exon 5) of the SMC2 gene. This alteration results from a A to G substitution at nucleotide position 535, causing the isoleucine (I) at amino acid position 179 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at