rs139646526
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002968.3(SALL1):āc.472A>Gā(p.Ser158Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00218 in 1,517,888 control chromosomes in the GnomAD database, including 11 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 Likely benign (ā ā ).
Frequency
Consequence
NM_002968.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SALL1 | NM_002968.3 | c.472A>G | p.Ser158Gly | missense_variant | 2/3 | ENST00000251020.9 | NP_002959.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SALL1 | ENST00000251020.9 | c.472A>G | p.Ser158Gly | missense_variant | 2/3 | 1 | NM_002968.3 | ENSP00000251020 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00385 AC: 582AN: 151094Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00135 AC: 330AN: 243684Hom.: 0 AF XY: 0.00138 AC XY: 183AN XY: 132414
GnomAD4 exome AF: 0.00200 AC: 2733AN: 1366678Hom.: 6 Cov.: 43 AF XY: 0.00200 AC XY: 1360AN XY: 679754
GnomAD4 genome AF: 0.00384 AC: 581AN: 151210Hom.: 5 Cov.: 32 AF XY: 0.00365 AC XY: 270AN XY: 73920
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 20, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 22, 2015 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | SALL1: BP4, BS2 - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
SALL1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 23, 2021 | 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). - |
Townes syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 28, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at