chr20-32453754-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001256798.2(NOL4L):c.1127C>A(p.Pro376His) variant causes a missense change. The variant allele was found at a frequency of 0.000194 in 1,552,926 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts 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. P376R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001256798.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOL4L | NM_001256798.2 | c.1127C>A | p.Pro376His | missense_variant | 7/11 | ENST00000621426.7 | |
NOL4L | NM_080616.6 | c.395C>A | p.Pro132His | missense_variant | 4/8 | ||
NOL4L | NM_001351680.2 | c.395C>A | p.Pro132His | missense_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOL4L | ENST00000621426.7 | c.1127C>A | p.Pro376His | missense_variant | 7/11 | 5 | NM_001256798.2 | P1 | |
NOL4L | ENST00000359676.9 | c.395C>A | p.Pro132His | missense_variant | 4/8 | 2 | |||
NOL4L | ENST00000475781.1 | c.465C>A | p.Pro155= | synonymous_variant, NMD_transcript_variant | 5/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 152128Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000213 AC: 33AN: 155084Hom.: 0 AF XY: 0.000122 AC XY: 10AN XY: 81810
GnomAD4 exome AF: 0.000197 AC: 276AN: 1400682Hom.: 1 Cov.: 32 AF XY: 0.000185 AC XY: 128AN XY: 690958
GnomAD4 genome ? AF: 0.000171 AC: 26AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.000228 AC XY: 17AN XY: 74418
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2021 | The c.395C>A (p.P132H) alteration is located in exon 4 (coding exon 3) of the NOL4L gene. This alteration results from a C to A substitution at nucleotide position 395, causing the proline (P) at amino acid position 132 to be replaced by a histidine (H). 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