rs587777290
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely pathogenic. The variant received 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5
The NM_173849.3(GSC):c.355+1G>C variant causes a splice donor, intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
GSC
NM_173849.3 splice_donor, intron
NM_173849.3 splice_donor, intron
Scores
3
3
1
Splicing: ADA: 1.000
2
Clinical Significance
Conservation
PhyloP100: 4.54
Publications
0 publications found
Genes affected
GSC (HGNC:4612): (goosecoid homeobox) This gene encodes a member of the bicoid subfamily of the paired (PRD) homeobox family of proteins. The encoded protein acts as a transcription factor and may be autoregulatory. A similar protein in mice plays a role in craniofacial and rib cage development during embryogenesis. [provided by RefSeq, Jul 2008]
GSC Gene-Disease associations (from GenCC):
- short stature-auditory canal atresia-mandibular hypoplasia-skeletal anomalies syndromeInheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_pathogenic. The variant received 7 ACMG points.
PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.5852713 fraction of the gene.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 14-94769660-C-G is Pathogenic according to our data. Variant chr14-94769660-C-G is described in ClinVar as Pathogenic. ClinVar VariationId is 126524.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1283452Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 629722
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1283452
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
629722
African (AFR)
AF:
AC:
0
AN:
25244
American (AMR)
AF:
AC:
0
AN:
18902
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
20320
East Asian (EAS)
AF:
AC:
0
AN:
30026
South Asian (SAS)
AF:
AC:
0
AN:
63276
European-Finnish (FIN)
AF:
AC:
0
AN:
31770
Middle Eastern (MID)
AF:
AC:
0
AN:
3720
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1037102
Other (OTH)
AF:
AC:
0
AN:
53092
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Short stature-auditory canal atresia-mandibular hypoplasia-skeletal anomalies syndrome Pathogenic:1
Dec 05, 2013
OMIM
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:literature only
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
PhyloP100
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DL_spliceai
Position offset: 1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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