rs74315427
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_020436.5(SALL4):c.1849C>T(p.Arg617Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. R617R) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_020436.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SALL4 | NM_020436.5 | c.1849C>T | p.Arg617Ter | stop_gained | 2/4 | ENST00000217086.9 | |
SALL4 | XM_047440318.1 | c.1543C>T | p.Arg515Ter | stop_gained | 2/4 | ||
SALL4 | NM_001318031.2 | c.1150+699C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SALL4 | ENST00000217086.9 | c.1849C>T | p.Arg617Ter | stop_gained | 2/4 | 1 | NM_020436.5 | P1 | |
SALL4 | ENST00000371539.7 | c.131-1493C>T | intron_variant | 1 | |||||
SALL4 | ENST00000395997.3 | c.1150+699C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461888Hom.: 0 Cov.: 72 AF XY: 0.00 AC XY: 0AN XY: 727244
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Duane-radial ray syndrome Pathogenic:2
Pathogenic, criteria provided, single submitter | research | HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology | Oct 08, 2019 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 26, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at