rs6091375
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020436.5(SALL4):āc.2392A>Cā(p.Ile798Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0544 in 1,614,114 control chromosomes in the GnomAD database, including 2,966 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_020436.5 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 |
---|---|---|---|---|---|---|---|
SALL4 | NM_020436.5 | c.2392A>C | p.Ile798Leu | missense_variant | 2/4 | ENST00000217086.9 | |
SALL4 | XM_047440318.1 | c.2086A>C | p.Ile696Leu | missense_variant | 2/4 | ||
SALL4 | NM_001318031.2 | c.1151-950A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SALL4 | ENST00000217086.9 | c.2392A>C | p.Ile798Leu | missense_variant | 2/4 | 1 | NM_020436.5 | P1 | |
SALL4 | ENST00000371539.7 | c.131-950A>C | intron_variant | 1 | |||||
SALL4 | ENST00000395997.3 | c.1151-950A>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0768 AC: 11680AN: 152120Hom.: 632 Cov.: 32
GnomAD3 exomes AF: 0.0476 AC: 11968AN: 251482Hom.: 476 AF XY: 0.0455 AC XY: 6186AN XY: 135916
GnomAD4 exome AF: 0.0520 AC: 76044AN: 1461876Hom.: 2330 Cov.: 31 AF XY: 0.0509 AC XY: 37040AN XY: 727240
GnomAD4 genome AF: 0.0769 AC: 11706AN: 152238Hom.: 636 Cov.: 32 AF XY: 0.0740 AC XY: 5506AN XY: 74422
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Duane-radial ray syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at