5-150521415-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001543.5(NDST1):āc.161C>Gā(p.Pro54Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000279 in 1,613,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001543.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NDST1 | ENST00000261797.7 | c.161C>G | p.Pro54Arg | missense_variant | Exon 2 of 15 | 1 | NM_001543.5 | ENSP00000261797.6 | ||
NDST1 | ENST00000523767.5 | c.161C>G | p.Pro54Arg | missense_variant | Exon 2 of 14 | 2 | ENSP00000428604.1 | |||
NDST1 | ENST00000519157.1 | c.161C>G | p.Pro54Arg | missense_variant | Exon 2 of 2 | 5 | ENSP00000427813.1 | |||
NDST1 | ENST00000522491.1 | c.161C>G | p.Pro54Arg | missense_variant | Exon 2 of 2 | 2 | ENSP00000429966.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000524 AC: 13AN: 247888Hom.: 0 AF XY: 0.0000521 AC XY: 7AN XY: 134334
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1460854Hom.: 0 Cov.: 31 AF XY: 0.0000330 AC XY: 24AN XY: 726802
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
not provided Uncertain:1
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at