rs1555635272
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_000271.5(NPC1):c.1686G>A(p.Val562=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,726 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. V562V) has been classified as Likely benign.
Frequency
Consequence
NM_000271.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPC1 | NM_000271.5 | c.1686G>A | p.Val562= | synonymous_variant | 11/25 | ENST00000269228.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPC1 | ENST00000269228.10 | c.1686G>A | p.Val562= | synonymous_variant | 11/25 | 1 | NM_000271.5 | P1 | |
NPC1 | ENST00000591051.1 | c.836-2928G>A | intron_variant | 2 | |||||
NPC1 | ENST00000540608.5 | n.1600G>A | non_coding_transcript_exon_variant | 9/16 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459726Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 726322
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Niemann-Pick disease, type C1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Oct 11, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at