chr18-78992109-G-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_171999.4(SALL3):āc.118G>Cā(p.Gly40Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000279 in 1,433,200 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 (ā ).
Frequency
Genomes: not found (cov: 33)
Exomes š: 0.0000028 ( 0 hom. )
Consequence
SALL3
NM_171999.4 missense
NM_171999.4 missense
Scores
9
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.35
Genes affected
SALL3 (HGNC:10527): (spalt like transcription factor 3) This gene encodes a sal-like C2H2-type zinc-finger protein, and belongs to a family of evolutionarily conserved genes found in species as diverse as Drosophila, C. elegans, and vertebrates. Mutations in some of these genes are associated with congenital disorders in human, suggesting their importance in embryonic development. This protein binds to DNA methyltransferase 3 alpha (DNMT3A), and reduces DNMT3A-mediated CpG island methylation. It is suggested that silencing of this gene, resulting in acceleration of DNA methylation, may have a role in oncogenesis. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.30616456).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SALL3 | NM_171999.4 | c.118G>C | p.Gly40Arg | missense_variant | 2/3 | ENST00000537592.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SALL3 | ENST00000537592.7 | c.118G>C | p.Gly40Arg | missense_variant | 2/3 | 5 | NM_171999.4 | P1 | |
SALL3 | ENST00000575389.6 | c.118G>C | p.Gly40Arg | missense_variant | 2/4 | 5 | |||
SALL3 | ENST00000536229.7 | c.-282G>C | 5_prime_UTR_variant | 1/3 | 3 | ||||
SALL3 | ENST00000572928.1 | n.97G>C | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD3 exomes AF: 0.00000477 AC: 1AN: 209766Hom.: 0 AF XY: 0.00000875 AC XY: 1AN XY: 114252
GnomAD3 exomes
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GnomAD4 exome AF: 0.00000279 AC: 4AN: 1433200Hom.: 0 Cov.: 29 AF XY: 0.00000282 AC XY: 2AN XY: 710426
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GnomAD4 genome Cov.: 33
GnomAD4 genome
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33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M;M
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
.;.;D
REVEL
Benign
Sift
Uncertain
.;.;D
Sift4G
Uncertain
D;T;T
Polyphen
0.98
.;.;D
Vest4
MutPred
Loss of helix (P = 0.079);Loss of helix (P = 0.079);Loss of helix (P = 0.079);
MVP
MPC
0.47
ClinPred
D
GERP RS
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at