9-98056861-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_018946.4(NANS):c.53C>T(p.Pro18Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0018 in 1,612,304 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P18A) has been classified as Uncertain significance.
Frequency
Consequence
NM_018946.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NANS | ENST00000210444.6 | c.53C>T | p.Pro18Leu | missense_variant | Exon 1 of 6 | 1 | NM_018946.4 | ENSP00000210444.5 | ||
NANS | ENST00000480925.1 | n.92C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 | |||||
NANS | ENST00000495319.1 | n.94C>T | non_coding_transcript_exon_variant | Exon 1 of 5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00163 AC: 248AN: 152240Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00198 AC: 487AN: 245624Hom.: 1 AF XY: 0.00202 AC XY: 270AN XY: 133772
GnomAD4 exome AF: 0.00182 AC: 2660AN: 1459950Hom.: 7 Cov.: 39 AF XY: 0.00170 AC XY: 1237AN XY: 726366
GnomAD4 genome AF: 0.00163 AC: 248AN: 152354Hom.: 0 Cov.: 34 AF XY: 0.00175 AC XY: 130AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:1
- -
NANS-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at