rs78871927
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003793.4(CTSF):c.722-5C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0772 in 1,613,818 control chromosomes in the GnomAD database, including 6,046 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 Benign (★★).
Frequency
Consequence
NM_003793.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTSF | NM_003793.4 | c.722-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000310325.10 | |||
CTSF | XM_011545328.3 | c.542-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTSF | ENST00000310325.10 | c.722-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_003793.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0700 AC: 10633AN: 152004Hom.: 642 Cov.: 32
GnomAD3 exomes AF: 0.0871 AC: 21863AN: 251142Hom.: 1308 AF XY: 0.0877 AC XY: 11897AN XY: 135730
GnomAD4 exome AF: 0.0779 AC: 113929AN: 1461696Hom.: 5399 Cov.: 35 AF XY: 0.0786 AC XY: 57124AN XY: 727132
GnomAD4 genome ? AF: 0.0700 AC: 10649AN: 152122Hom.: 647 Cov.: 32 AF XY: 0.0766 AC XY: 5692AN XY: 74330
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Oct 26, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 20, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 17, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Neuronal ceroid lipofuscinosis 13 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at