14-21523209-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001364564.1(SALL2):āc.2513C>Gā(p.Pro838Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00202 in 1,614,038 control chromosomes in the GnomAD database, including 57 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 ).
Frequency
Consequence
NM_001364564.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SALL2 | NM_001364564.1 | c.2513C>G | p.Pro838Arg | missense_variant | 2/2 | ENST00000537235.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SALL2 | ENST00000537235.2 | c.2513C>G | p.Pro838Arg | missense_variant | 2/2 | 2 | NM_001364564.1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0109 AC: 1661AN: 152098Hom.: 32 Cov.: 32
GnomAD3 exomes AF: 0.00277 AC: 697AN: 251382Hom.: 14 AF XY: 0.00217 AC XY: 295AN XY: 135858
GnomAD4 exome AF: 0.00110 AC: 1602AN: 1461822Hom.: 25 Cov.: 34 AF XY: 0.000920 AC XY: 669AN XY: 727206
GnomAD4 genome ? AF: 0.0109 AC: 1660AN: 152216Hom.: 32 Cov.: 32 AF XY: 0.0107 AC XY: 796AN XY: 74418
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at