chr2-17665599-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001142286.2(SMC6):c.3176G>C(p.Ser1059Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000435 in 1,607,886 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_001142286.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMC6 | NM_001142286.2 | c.3176G>C | p.Ser1059Thr | missense_variant | 28/28 | ENST00000448223.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMC6 | ENST00000448223.7 | c.3176G>C | p.Ser1059Thr | missense_variant | 28/28 | 1 | NM_001142286.2 | P1 | |
SMC6 | ENST00000351948.8 | c.3176G>C | p.Ser1059Thr | missense_variant | 27/27 | 1 | P1 | ||
SMC6 | ENST00000402989.5 | c.3176G>C | p.Ser1059Thr | missense_variant | 30/30 | 2 | P1 | ||
SMC6 | ENST00000481708.1 | n.3424G>C | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248210Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134260
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1455796Hom.: 0 Cov.: 28 AF XY: 0.00000414 AC XY: 3AN XY: 724324
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.3176G>C (p.S1059T) alteration is located in exon 28 (coding exon 26) of the SMC6 gene. This alteration results from a G to C substitution at nucleotide position 3176, causing the serine (S) at amino acid position 1059 to be replaced by a threonine (T). 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