14-21523010-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001364564.1(SALL2):āc.2712G>Cā(p.Glu904Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00981 in 1,614,116 control chromosomes in the GnomAD database, including 1,245 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_001364564.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SALL2 | NM_001364564.1 | c.2712G>C | p.Glu904Asp | missense_variant | 2/2 | ENST00000537235.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SALL2 | ENST00000537235.2 | c.2712G>C | p.Glu904Asp | missense_variant | 2/2 | 2 | NM_001364564.1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0509 AC: 7748AN: 152138Hom.: 615 Cov.: 32
GnomAD3 exomes AF: 0.0137 AC: 3447AN: 251452Hom.: 265 AF XY: 0.00995 AC XY: 1352AN XY: 135894
GnomAD4 exome AF: 0.00550 AC: 8044AN: 1461860Hom.: 622 Cov.: 34 AF XY: 0.00482 AC XY: 3505AN XY: 727230
GnomAD4 genome ? AF: 0.0512 AC: 7789AN: 152256Hom.: 623 Cov.: 32 AF XY: 0.0497 AC XY: 3702AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
SALL2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 23, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at