rs492899
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000375394.7(SKIC2):c.1972-42T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 1,252,492 control chromosomes in the GnomAD database, including 9,645 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.15 ( 2235 hom., cov: 33)
Exomes 𝑓: 0.10 ( 7410 hom. )
Consequence
SKIC2
ENST00000375394.7 intron
ENST00000375394.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.30
Genes affected
SKIC2 (HGNC:10898): (SKI2 subunit of superkiller complex) DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which is a human homologue of yeast SKI2 and may be involved in antiviral activity by blocking translation of poly(A) deficient mRNAs. This gene is located in the class III region of the major histocompatibility complex. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 6-31965741-T-C is Benign according to our data. Variant chr6-31965741-T-C is described in ClinVar as [Benign]. Clinvar id is 1228348.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SKIC2 | NM_006929.5 | c.1972-42T>C | intron_variant | ENST00000375394.7 | NP_008860.4 | |||
SKIC2 | XM_011514815.4 | c.1972-42T>C | intron_variant | XP_011513117.1 | ||||
SKIC2 | XM_047419259.1 | c.1972-42T>C | intron_variant | XP_047275215.1 | ||||
SKIC2 | XM_047419260.1 | c.1972-42T>C | intron_variant | XP_047275216.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SKIC2 | ENST00000375394.7 | c.1972-42T>C | intron_variant | 1 | NM_006929.5 | ENSP00000364543 | P1 |
Frequencies
GnomAD3 genomes AF: 0.150 AC: 22847AN: 152086Hom.: 2224 Cov.: 33
GnomAD3 genomes
AF:
AC:
22847
AN:
152086
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.119 AC: 27925AN: 235250Hom.: 2211 AF XY: 0.123 AC XY: 15763AN XY: 127728
GnomAD3 exomes
AF:
AC:
27925
AN:
235250
Hom.:
AF XY:
AC XY:
15763
AN XY:
127728
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.102 AC: 112265AN: 1100288Hom.: 7410 Cov.: 15 AF XY: 0.106 AC XY: 59481AN XY: 558796
GnomAD4 exome
AF:
AC:
112265
AN:
1100288
Hom.:
Cov.:
15
AF XY:
AC XY:
59481
AN XY:
558796
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.150 AC: 22899AN: 152204Hom.: 2235 Cov.: 33 AF XY: 0.154 AC XY: 11463AN XY: 74432
GnomAD4 genome
AF:
AC:
22899
AN:
152204
Hom.:
Cov.:
33
AF XY:
AC XY:
11463
AN XY:
74432
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
649
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Trichohepatoenteric syndrome 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at