chr16-11548733-C-T
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001136472.2(LITAF):c.*904G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000377 in 453,472 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001136472.2 3_prime_UTR
Scores
Clinical Significance
Conservation
Publications
- Charcot-Marie-Tooth disease type 1CInheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
- Charcot-Marie-Tooth diseaseInheritance: AD Classification: MODERATE Submitted by: ClinGen
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ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LITAF | ENST00000622633.5 | c.*904G>A | 3_prime_UTR_variant | Exon 4 of 4 | 1 | NM_001136472.2 | ENSP00000483114.1 | |||
LITAF | ENST00000339430.9 | c.*904G>A | 3_prime_UTR_variant | Exon 4 of 4 | 1 | ENSP00000340118.5 | ||||
LITAF | ENST00000571688.6 | c.*904G>A | 3_prime_UTR_variant | Exon 4 of 4 | 1 | ENSP00000459533.1 | ||||
LITAF | ENST00000413364.6 | c.*1029G>A | 3_prime_UTR_variant | Exon 5 of 5 | 2 | ENSP00000397958.2 |
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 151886Hom.: 1 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.00105 AC: 136AN: 130092 AF XY: 0.00103 show subpopulations
GnomAD4 exome AF: 0.000395 AC: 119AN: 301468Hom.: 1 Cov.: 0 AF XY: 0.000390 AC XY: 67AN XY: 171780 show subpopulations
GnomAD4 genome AF: 0.000342 AC: 52AN: 152004Hom.: 1 Cov.: 31 AF XY: 0.000444 AC XY: 33AN XY: 74272 show subpopulations
ClinVar
Submissions by phenotype
Charcot-Marie-Tooth disease type 1C Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at