Genetic Variant SKI:p.Gly33Gly (chr1-2228865-C-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_003036.4(SKI):c.99C>G(p.Gly33Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0206 in 1,428,256 control chromosomes in the GnomAD database, including 365 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. G33G) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.013 ( 27 hom., cov: 31)

Exomes 𝑓: 0.021 ( 338 hom. )

Consequence

SKI
NM_003036.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:13

Conservation

PhyloP100: 0.911

Publications

3 publications found

Variant links:

Genes affected

SKI (HGNC:10896): (SKI proto-oncogene) This gene encodes the nuclear protooncogene protein homolog of avian sarcoma viral (v-ski) oncogene. It functions as a repressor of TGF-beta signaling, and may play a role in neural tube development and muscle differentiation. [provided by RefSeq, Oct 2009]

SKI Gene-Disease associations (from GenCC):

Shprintzen-Goldberg syndrome
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), PanelApp Australia, G2P, Orphanet, Genomics England PanelApp, ClinGen

SKI links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 1-2228865-C-G is Benign according to our data. Variant chr1-2228865-C-G is described in ClinVar as Benign. ClinVar VariationId is 139112.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.911 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0134 (2005/149744) while in subpopulation NFE AF = 0.0213 (1429/67008). AF 95% confidence interval is 0.0204. There are 27 homozygotes in GnomAd4. There are 932 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.

BS2

High AC in GnomAd4 at 2005 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003036.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SKI	NM_003036.4	MANE Select	c.99C>G	p.Gly33Gly	synonymous	Exon 1 of 7	NP_003027.1	P12755

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SKI	ENST00000378536.5	TSL:1 MANE Select	c.99C>G	p.Gly33Gly	synonymous	Exon 1 of 7	ENSP00000367797.4	P12755
SKI	ENST00000851187.1		c.99C>G	p.Gly33Gly	synonymous	Exon 1 of 7	ENSP00000521247.1
SKI	ENST00000704337.1		n.137+1341C>G		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0134

AC:

2005

AN:

149638

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00367

Gnomad AMI

AF:

0.00440

Gnomad AMR

AF:

0.0109

Gnomad ASJ

AF:

0.0126

Gnomad EAS

AF:

0.000195

Gnomad SAS

AF:

0.00456

Gnomad FIN

AF:

0.0153

Gnomad MID

AF:

0.0160

Gnomad NFE

AF:

0.0213

Gnomad OTH

AF:

0.0170

GnomAD2 exomes

AF:

0.0133

AC:

1267

AN:

95400

AF XY:

0.0129

show subpopulations

Gnomad AFR exome

AF:

0.00284

Gnomad AMR exome

AF:

0.00946

Gnomad ASJ exome

AF:

0.0156

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0187

Gnomad NFE exome

AF:

0.0198

Gnomad OTH exome

AF:

0.0140

GnomAD4 exome

AF:

0.0214

AC:

27383

AN:

1278512

Hom.:

338

Cov.:

AF XY:

0.0210

AC XY:

13258

AN XY:

631882

show subpopulations

African (AFR)

AF:

0.00293

AC:

AN:

26264

American (AMR)

AF:

0.0107

AC:

283

AN:

26348

Ashkenazi Jewish (ASJ)

AF:

0.0156

AC:

327

AN:

21004

East Asian (EAS)

AF:

0.00

AC:

AN:

26448

South Asian (SAS)

AF:

0.00504

AC:

363

AN:

71986

European-Finnish (FIN)

AF:

0.0165

AC:

522

AN:

31660

Middle Eastern (MID)

AF:

0.0153

AC:

AN:

3720

European-Non Finnish (NFE)

AF:

0.0243

AC:

24788

AN:

1019974

Other (OTH)

AF:

0.0189

AC:

966

AN:

51108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

1218

2435

3653

4870

6088

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1016

2032

3048

4064

5080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0134

AC:

2005

AN:

149744

Hom.:

Cov.:

AF XY:

0.0128

AC XY:

932

AN XY:

73052

show subpopulations

African (AFR)

AF:

0.00366

AC:

151

AN:

41236

American (AMR)

AF:

0.0109

AC:

164

AN:

15100

Ashkenazi Jewish (ASJ)

AF:

0.0126

AC:

AN:

3422

East Asian (EAS)

AF:

0.000196

AC:

AN:

5102

South Asian (SAS)

AF:

0.00478

AC:

AN:

4816

European-Finnish (FIN)

AF:

0.0153

AC:

150

AN:

9776

Middle Eastern (MID)

AF:

0.0172

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.0213

AC:

1429

AN:

67008

Other (OTH)

AF:

0.0168

AC:

AN:

2084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

100

200

301

401

501

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0173

Hom.:

Bravo

AF:

0.0138

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (8)

Shprintzen-Goldberg syndrome (3)

Familial thoracic aortic aneurysm and aortic dissection (1)

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

(source)

DANN

Benign

0.69

PhyloP100

0.91

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over