9-104102017-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_006444.3(SMC2):c.694C>T(p.Arg232Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000685 in 1,458,850 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 (★).
Frequency
Consequence
NM_006444.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMC2 | ENST00000374793.8 | c.694C>T | p.Arg232Cys | missense_variant | Exon 8 of 25 | 1 | NM_006444.3 | ENSP00000363925.3 | ||
SMC2 | ENST00000286398.11 | c.694C>T | p.Arg232Cys | missense_variant | Exon 8 of 25 | 1 | ENSP00000286398.7 | |||
SMC2 | ENST00000374787.7 | c.694C>T | p.Arg232Cys | missense_variant | Exon 8 of 25 | 2 | ENSP00000363919.3 | |||
SMC2 | ENST00000440179.5 | c.259C>T | p.Arg87Cys | missense_variant | Exon 6 of 6 | 3 | ENSP00000414999.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1458850Hom.: 0 Cov.: 30 AF XY: 0.00000551 AC XY: 4AN XY: 725620
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.694C>T (p.R232C) alteration is located in exon 8 (coding exon 7) of the SMC2 gene. This alteration results from a C to T substitution at nucleotide position 694, causing the arginine (R) at amino acid position 232 to be replaced by a cysteine (C). 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