chr9-104100202-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006444.3(SMC2):c.590C>T(p.Thr197Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00005 in 1,518,702 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006444.3 missense, splice_region
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.590C>T | p.Thr197Met | missense_variant, splice_region_variant | 6/25 | ENST00000374793.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMC2 | ENST00000374793.8 | c.590C>T | p.Thr197Met | missense_variant, splice_region_variant | 6/25 | 1 | NM_006444.3 | P1 | |
SMC2 | ENST00000286398.11 | c.590C>T | p.Thr197Met | missense_variant, splice_region_variant | 6/25 | 1 | P1 | ||
SMC2 | ENST00000374787.7 | c.590C>T | p.Thr197Met | missense_variant, splice_region_variant | 6/25 | 2 | P1 | ||
SMC2 | ENST00000440179.5 | c.155C>T | p.Thr52Met | missense_variant, splice_region_variant | 4/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 151984Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000840 AC: 17AN: 202342Hom.: 0 AF XY: 0.0000359 AC XY: 4AN XY: 111362
GnomAD4 exome AF: 0.0000527 AC: 72AN: 1366718Hom.: 0 Cov.: 24 AF XY: 0.0000396 AC XY: 27AN XY: 682468
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 151984Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74224
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 28, 2022 | The c.590C>T (p.T197M) alteration is located in exon 6 (coding exon 5) of the SMC2 gene. This alteration results from a C to T substitution at nucleotide position 590, causing the threonine (T) at amino acid position 197 to be replaced by a methionine (M). 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