8-38304680-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_023034.2(NSD3):c.2518G>A(p.Val840Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_023034.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NSD3 | NM_023034.2 | c.2518G>A | p.Val840Ile | missense_variant | 14/24 | ENST00000317025.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NSD3 | ENST00000317025.13 | c.2518G>A | p.Val840Ile | missense_variant | 14/24 | 1 | NM_023034.2 | P4 | |
NSD3 | ENST00000527502.5 | c.2518G>A | p.Val840Ile | missense_variant | 14/24 | 1 | |||
NSD3 | ENST00000433384.6 | c.2518G>A | p.Val840Ile | missense_variant | 14/23 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461760Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727182
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 30, 2023 | The c.2518G>A (p.V840I) alteration is located in exon 14 (coding exon 13) of the WHSC1L1 gene. This alteration results from a G to A substitution at nucleotide position 2518, causing the valine (V) at amino acid position 840 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at