Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PM2_SupportingBP4_Moderate
The NM_002968.3(SALL1):c.3843C>G(p.Asn1281Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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Verdict is Likely_benign. Variant got -1 ACMG points.
GnomAD3 genomesCov.: 32
Submissions by phenotype
|Uncertain significance, criteria provided, single submitter
|Mar 27, 2023
|In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬† is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 1358915). This variant has not been reported in the literature in individuals affected with SALL1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 1281 of the SALL1 protein (p.Asn1281Lys). -
Find out detailed SpliceAI scores and Pangolin per-transcript scores at