5-150540205-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_001543.5(NDST1):āc.1690G>Cā(p.Val564Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000651 in 1,614,020 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V564M) has been classified as Uncertain significance.
Frequency
Consequence
NM_001543.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDST1 | NM_001543.5 | c.1690G>C | p.Val564Leu | missense_variant | 8/15 | ENST00000261797.7 | |
NDST1 | NM_001301063.2 | c.1690G>C | p.Val564Leu | missense_variant | 8/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDST1 | ENST00000261797.7 | c.1690G>C | p.Val564Leu | missense_variant | 8/15 | 1 | NM_001543.5 | P1 | |
NDST1 | ENST00000523767.5 | c.1690G>C | p.Val564Leu | missense_variant | 8/14 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000916 AC: 23AN: 251066Hom.: 1 AF XY: 0.000133 AC XY: 18AN XY: 135708
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461806Hom.: 4 Cov.: 35 AF XY: 0.0000894 AC XY: 65AN XY: 727192
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 04, 2018 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.1690G>C (p.V564L) alteration is located in exon 8 (coding exon 7) of the NDST1 gene. This alteration results from a G to C substitution at nucleotide position 1690, causing the valine (V) at amino acid position 564 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2017 | - - |
Intellectual disability, autosomal recessive 46 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at