chr20-32456165-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001256798.2(NOL4L):c.1072G>A(p.Asp358Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000158 in 1,579,038 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D358E) has been classified as Uncertain significance.
Frequency
Consequence
NM_001256798.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOL4L | NM_001256798.2 | c.1072G>A | p.Asp358Asn | missense_variant | 6/11 | ENST00000621426.7 | |
NOL4L | NM_080616.6 | c.340G>A | p.Asp114Asn | missense_variant | 3/8 | ||
NOL4L | NM_001351680.2 | c.340G>A | p.Asp114Asn | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOL4L | ENST00000621426.7 | c.1072G>A | p.Asp358Asn | missense_variant | 6/11 | 5 | NM_001256798.2 | P1 | |
NOL4L | ENST00000359676.9 | c.340G>A | p.Asp114Asn | missense_variant | 3/8 | 2 | |||
NOL4L | ENST00000475781.1 | c.340G>A | p.Asp114Asn | missense_variant, NMD_transcript_variant | 3/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152272Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000890 AC: 2AN: 224730Hom.: 0 AF XY: 0.0000164 AC XY: 2AN XY: 121938
GnomAD4 exome AF: 0.0000147 AC: 21AN: 1426766Hom.: 0 Cov.: 31 AF XY: 0.0000212 AC XY: 15AN XY: 706886
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152272Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74392
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2022 | The c.340G>A (p.D114N) alteration is located in exon 3 (coding exon 2) of the NOL4L gene. This alteration results from a G to A substitution at nucleotide position 340, causing the aspartic acid (D) at amino acid position 114 to be replaced by an asparagine (N). 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