7-44539581-G-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001101648.2(NPC1L1):c.816C>G(p.Leu272Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 1,613,858 control chromosomes in the GnomAD database, including 45,308 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001101648.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NPC1L1 | NM_001101648.2 | c.816C>G | p.Leu272Leu | synonymous_variant | Exon 2 of 19 | ENST00000381160.8 | NP_001095118.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPC1L1 | ENST00000381160.8 | c.816C>G | p.Leu272Leu | synonymous_variant | Exon 2 of 19 | 1 | NM_001101648.2 | ENSP00000370552.3 | ||
NPC1L1 | ENST00000289547.8 | c.816C>G | p.Leu272Leu | synonymous_variant | Exon 2 of 20 | 1 | ENSP00000289547.4 | |||
NPC1L1 | ENST00000546276.5 | c.816C>G | p.Leu272Leu | synonymous_variant | Exon 2 of 18 | 1 | ENSP00000438033.1 | |||
NPC1L1 | ENST00000423141.1 | c.816C>G | p.Leu272Leu | synonymous_variant | Exon 2 of 7 | 1 | ENSP00000404670.1 |
Frequencies
GnomAD3 genomes AF: 0.236 AC: 35859AN: 152028Hom.: 4472 Cov.: 33
GnomAD3 exomes AF: 0.249 AC: 62483AN: 250938Hom.: 8143 AF XY: 0.245 AC XY: 33205AN XY: 135688
GnomAD4 exome AF: 0.232 AC: 339457AN: 1461712Hom.: 40825 Cov.: 40 AF XY: 0.231 AC XY: 168147AN XY: 727134
GnomAD4 genome AF: 0.236 AC: 35902AN: 152146Hom.: 4483 Cov.: 33 AF XY: 0.244 AC XY: 18129AN XY: 74364
ClinVar
Submissions by phenotype
not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
Statins, attenuated cholesterol lowering by Other:1
- likely responsive
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at