rs369271997
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_015909.4(NBAS):c.5129C>T(p.Thr1710Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000565 in 1,609,346 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T1710T) has been classified as Likely benign.
Frequency
Consequence
NM_015909.4 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 |
---|---|---|---|---|---|---|---|
NBAS | NM_015909.4 | c.5129C>T | p.Thr1710Met | missense_variant | 42/52 | ENST00000281513.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NBAS | ENST00000281513.10 | c.5129C>T | p.Thr1710Met | missense_variant | 42/52 | 1 | NM_015909.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251420Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135884
GnomAD4 exome AF: 0.0000597 AC: 87AN: 1457136Hom.: 0 Cov.: 31 AF XY: 0.0000607 AC XY: 44AN XY: 725248
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74364
ClinVar
Submissions by phenotype
Short stature-optic atrophy-Pelger-HuC+t anomaly syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | research | TIDEX, University of British Columbia | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at