Variant rs429608 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006929.5(SKIC2):c.1212-29G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 1,607,370 control chromosomes in the GnomAD database, including 19,940 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.16 ( 2093 hom., cov: 31)

Exomes 𝑓: 0.15 ( 17847 hom. )

Consequence

SKIC2
NM_006929.5 intron

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: 1.34

Variant links:

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]

SKIC2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
SKIC2	NM_006929.5 linkuse as main transcript	c.1212-29G>A	intron_variant	ENST00000375394.7
SKIC2	XM_011514815.4 linkuse as main transcript	c.1212-29G>A	intron_variant
SKIC2	XM_047419259.1 linkuse as main transcript	c.1212-29G>A	intron_variant
SKIC2	XM_047419260.1 linkuse as main transcript	c.1212-29G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SKIC2	ENST00000375394.7 linkuse as main transcript	c.1212-29G>A		intron_variant		1	NM_006929.5	P1

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24462

AN:

151900

Hom.:

2093

Cov.:

show subpopulations

Gnomad AFR

AF:

0.217

Gnomad AMI

AF:

0.0603

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.0963

Gnomad EAS

AF:

0.0837

Gnomad SAS

AF:

0.197

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.149

Gnomad OTH

AF:

0.167

GnomAD3 exomes

AF:

0.143

AC:

35468

AN:

248358

Hom.:

2828

AF XY:

0.148

AC XY:

19884

AN XY:

134760

show subpopulations

Gnomad AFR exome

AF:

0.213

Gnomad AMR exome

AF:

0.0989

Gnomad ASJ exome

AF:

0.0919

Gnomad EAS exome

AF:

0.0779

Gnomad SAS exome

AF:

0.218

Gnomad FIN exome

AF:

0.119

Gnomad NFE exome

AF:

0.146

Gnomad OTH exome

AF:

0.148

GnomAD4 exome

AF:

0.153

AC:

222530

AN:

1455352

Hom.:

17847

Cov.:

AF XY:

0.154

AC XY:

111637

AN XY:

724432

show subpopulations

Gnomad4 AFR exome

AF:

0.214

Gnomad4 AMR exome

AF:

0.103

Gnomad4 ASJ exome

AF:

0.0951

Gnomad4 EAS exome

AF:

0.0949

Gnomad4 SAS exome

AF:

0.210

Gnomad4 FIN exome

AF:

0.120

Gnomad4 NFE exome

AF:

0.153

Gnomad4 OTH exome

AF:

0.162

GnomAD4 genome

AF:

0.161

AC:

24489

AN:

152018

Hom.:

2093

Cov.:

AF XY:

0.159

AC XY:

11810

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.217

Gnomad4 AMR

AF:

0.133

Gnomad4 ASJ

AF:

0.0963

Gnomad4 EAS

AF:

0.0839

Gnomad4 SAS

AF:

0.195

Gnomad4 FIN

AF:

0.113

Gnomad4 NFE

AF:

0.149

Gnomad4 OTH

AF:

0.166

Alfa

AF:

0.139

Hom.:

3004

Bravo

AF:

0.164

Asia WGS

AF:

0.199

AC:

689

AN:

3478

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

LINK: link

Submissions by phenotype

not provided

Other:1

not provided, no classification provided

not provided

Department of Ophthalmology and Visual Sciences Kyoto University

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

DANN

Benign

0.78

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over