chr8-143792026-G-T
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM1PM2BP4
The NM_182706.5(SCRIB):c.4622C>A(p.Ser1541Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000934 in 1,563,530 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000096 ( 0 hom. )
Consequence
SCRIB
NM_182706.5 missense
NM_182706.5 missense
Scores
3
6
7
Clinical Significance
Conservation
PhyloP100: 7.06
Genes affected
SCRIB (HGNC:30377): (scribble planar cell polarity protein) This gene encodes a protein that was identified as being similar to the Drosophila scribble protein. The mammalian protein is involved in tumor suppression pathways. As a scaffold protein involved in cell polarization processes, this protein binds to many other proteins. The encoded protein binds to papillomavirus E6 protein via its PDZ domain and the C-terminus of E6. Two alternatively spliced transcript variants that encode different protein isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM1
In a modified_residue Phosphoserine (size 0) in uniprot entity SCRIB_HUMAN
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.26740766).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCRIB | NM_182706.5 | c.4622C>A | p.Ser1541Tyr | missense_variant | 33/37 | ENST00000356994.7 | |
SCRIB | NM_015356.5 | c.4622C>A | p.Ser1541Tyr | missense_variant | 33/36 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCRIB | ENST00000356994.7 | c.4622C>A | p.Ser1541Tyr | missense_variant | 33/37 | 2 | NM_182706.5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152154Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000297 AC: 5AN: 168172Hom.: 0 AF XY: 0.0000430 AC XY: 4AN XY: 92990
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GnomAD4 exome AF: 0.0000964 AC: 136AN: 1411376Hom.: 0 Cov.: 53 AF XY: 0.0000859 AC XY: 60AN XY: 698734
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GnomAD4 genome AF: 0.0000657 AC: 10AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74328
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 13, 2023 | The c.4622C>A (p.S1541Y) alteration is located in exon 33 (coding exon 33) of the SCRIB gene. This alteration results from a C to A substitution at nucleotide position 4622, causing the serine (S) at amino acid position 1541 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Pathogenic
D;D;D
Sift4G
Uncertain
D;D;D
Vest4
MutPred
Loss of glycosylation at S1541 (P = 0.0031);Loss of glycosylation at S1541 (P = 0.0031);.;
MVP
ClinPred
T
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gMVP
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at