NM_025099.6:c.3425T>A
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP5
The NM_025099.6(CTC1):c.3425T>A(p.Leu1142His) variant causes a missense change. The variant allele was found at a frequency of 0.0000384 in 1,614,092 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Synonymous variant affecting the same amino acid position (i.e. L1142L) has been classified as Likely benign.
Frequency
Consequence
NM_025099.6 missense
Scores
Clinical Significance
Conservation
Publications
- cerebroretinal microangiopathy with calcifications and cysts 1Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics, G2P
- dyskeratosis congenitaInheritance: AR, AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, Orphanet
- Coats plus syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152202Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000922 AC: 23AN: 249556 AF XY: 0.0000739 show subpopulations
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.0000371 AC XY: 27AN XY: 727246 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74360 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Cerebroretinal microangiopathy with calcifications and cysts 1 Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at