NM_025099.6:c.1207-4C>T
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_025099.6(CTC1):c.1207-4C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000519 in 1,606,484 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_025099.6 splice_region, intron
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: Likely_benign. The variant received -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000309 AC: 47AN: 152184Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000382 AC: 94AN: 245802 AF XY: 0.000366 show subpopulations
GnomAD4 exome AF: 0.000541 AC: 786AN: 1454182Hom.: 1 Cov.: 31 AF XY: 0.000510 AC XY: 369AN XY: 723474 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000309 AC: 47AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74474 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Dyskeratosis congenita Uncertain:1Benign:2
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
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Cerebroretinal microangiopathy with calcifications and cysts 1 Uncertain:2
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This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
not specified Benign:1
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not provided Benign:1
CTC1: BP4 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at