rs16975750
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005357.4(LIPE):āc.298T>Cā(p.Tyr100His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0133 in 1,614,018 control chromosomes in the GnomAD database, including 2,066 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005357.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIPE | NM_005357.4 | c.298T>C | p.Tyr100His | missense_variant | 1/10 | ENST00000244289.9 | |
LIPE-AS1 | NR_073180.1 | n.77+29628A>G | intron_variant, non_coding_transcript_variant | ||||
LIPE | XM_005258937.4 | c.298T>C | p.Tyr100His | missense_variant | 1/9 | ||
LIPE-AS1 | NR_073179.1 | n.1450+1648A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIPE | ENST00000244289.9 | c.298T>C | p.Tyr100His | missense_variant | 1/10 | 1 | NM_005357.4 | P1 | |
LIPE-AS1 | ENST00000594624.7 | n.66+29628A>G | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0656 AC: 9977AN: 152006Hom.: 1037 Cov.: 31
GnomAD3 exomes AF: 0.0185 AC: 4643AN: 251452Hom.: 477 AF XY: 0.0135 AC XY: 1828AN XY: 135902
GnomAD4 exome AF: 0.00778 AC: 11377AN: 1461894Hom.: 1019 Cov.: 32 AF XY: 0.00699 AC XY: 5083AN XY: 727248
GnomAD4 genome AF: 0.0659 AC: 10030AN: 152124Hom.: 1047 Cov.: 31 AF XY: 0.0643 AC XY: 4780AN XY: 74396
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | This variant is associated with the following publications: (PMID: 24555826) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at