rs3911893
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006929.5(SKIC2):c.2659G>A(p.Asp887Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0394 in 1,612,958 control chromosomes in the GnomAD database, including 1,696 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_006929.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SKIC2 | NM_006929.5 | c.2659G>A | p.Asp887Asn | missense_variant | 22/28 | ENST00000375394.7 | |
SKIC2 | XM_011514815.4 | c.2659G>A | p.Asp887Asn | missense_variant | 22/25 | ||
SKIC2 | XM_047419259.1 | c.2659G>A | p.Asp887Asn | missense_variant | 22/25 | ||
SKIC2 | XM_047419260.1 | c.2659G>A | p.Asp887Asn | missense_variant | 22/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SKIC2 | ENST00000375394.7 | c.2659G>A | p.Asp887Asn | missense_variant | 22/28 | 1 | NM_006929.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0553 AC: 8409AN: 152162Hom.: 287 Cov.: 32
GnomAD3 exomes AF: 0.0518 AC: 12769AN: 246348Hom.: 494 AF XY: 0.0489 AC XY: 6574AN XY: 134320
GnomAD4 exome AF: 0.0377 AC: 55109AN: 1460678Hom.: 1410 Cov.: 34 AF XY: 0.0374 AC XY: 27183AN XY: 726664
GnomAD4 genome ? AF: 0.0553 AC: 8415AN: 152280Hom.: 286 Cov.: 32 AF XY: 0.0548 AC XY: 4081AN XY: 74440
ClinVar
Submissions by phenotype
Trichohepatoenteric syndrome 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at