rs141599100
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_003635.4(NDST2):c.199C>T(p.Arg67Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000247 in 1,613,728 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 Likely benign (★).
Frequency
Consequence
NM_003635.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDST2 | NM_003635.4 | c.199C>T | p.Arg67Trp | missense_variant | 3/15 | ENST00000309979.11 | |
NDST2-ZSWIM8-AS1 | NR_182656.1 | n.992C>T | non_coding_transcript_exon_variant | 3/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDST2 | ENST00000309979.11 | c.199C>T | p.Arg67Trp | missense_variant | 3/15 | 1 | NM_003635.4 | P1 | |
NDST2 | ENST00000299641.8 | c.199C>T | p.Arg67Trp | missense_variant | 1/13 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000116 AC: 29AN: 249790Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135174
GnomAD4 exome AF: 0.000257 AC: 376AN: 1461492Hom.: 0 Cov.: 32 AF XY: 0.000219 AC XY: 159AN XY: 727020
GnomAD4 genome ? AF: 0.000145 AC: 22AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74360
ClinVar
Submissions by phenotype
Anophthalmia-microphthalmia syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Paul Sabatier University EA-4555, Paul Sabatier University | Jan 01, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at