7-44540234-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001101648.2(NPC1L1):c.163G>C(p.Val55Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,613,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_001101648.2 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 |
---|---|---|---|---|---|---|---|
NPC1L1 | NM_001101648.2 | c.163G>C | p.Val55Leu | missense_variant | 2/19 | ENST00000381160.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPC1L1 | ENST00000381160.8 | c.163G>C | p.Val55Leu | missense_variant | 2/19 | 1 | NM_001101648.2 | P1 | |
NPC1L1 | ENST00000289547.8 | c.163G>C | p.Val55Leu | missense_variant | 2/20 | 1 | |||
NPC1L1 | ENST00000546276.5 | c.163G>C | p.Val55Leu | missense_variant | 2/18 | 1 | |||
NPC1L1 | ENST00000423141.1 | c.163G>C | p.Val55Leu | missense_variant | 2/7 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152016Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251364Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135872
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461858Hom.: 0 Cov.: 34 AF XY: 0.0000151 AC XY: 11AN XY: 727236
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152016Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74246
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at