rs10264715
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001101648.2(NPC1L1):c.3792C>T(p.Tyr1264Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 1,613,972 control chromosomes in the GnomAD database, including 36,381 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.3792C>T | p.Tyr1264Tyr | synonymous_variant | Exon 18 of 19 | ENST00000381160.8 | NP_001095118.1 | |
NPC1L1 | NM_013389.3 | c.3873C>T | p.Tyr1291Tyr | synonymous_variant | Exon 19 of 20 | NP_037521.2 | ||
NPC1L1 | XM_011515326.4 | c.3597C>T | p.Tyr1199Tyr | synonymous_variant | Exon 17 of 18 | XP_011513628.1 | ||
NPC1L1 | XM_011515328.3 | c.2151C>T | p.Tyr717Tyr | synonymous_variant | Exon 15 of 16 | XP_011513630.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPC1L1 | ENST00000381160.8 | c.3792C>T | p.Tyr1264Tyr | synonymous_variant | Exon 18 of 19 | 1 | NM_001101648.2 | ENSP00000370552.3 | ||
NPC1L1 | ENST00000289547.8 | c.3873C>T | p.Tyr1291Tyr | synonymous_variant | Exon 19 of 20 | 1 | ENSP00000289547.4 | |||
NPC1L1 | ENST00000546276.5 | c.3654C>T | p.Tyr1218Tyr | synonymous_variant | Exon 17 of 18 | 1 | ENSP00000438033.1 |
Frequencies
GnomAD3 genomes AF: 0.158 AC: 24021AN: 152054Hom.: 2532 Cov.: 32
GnomAD3 exomes AF: 0.166 AC: 41709AN: 251038Hom.: 4542 AF XY: 0.169 AC XY: 22932AN XY: 135690
GnomAD4 exome AF: 0.206 AC: 301785AN: 1461800Hom.: 33850 Cov.: 36 AF XY: 0.204 AC XY: 148396AN XY: 727194
GnomAD4 genome AF: 0.158 AC: 24016AN: 152172Hom.: 2531 Cov.: 32 AF XY: 0.156 AC XY: 11606AN XY: 74374
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 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at