chr11-66566329-G-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_003793.4(CTSF):āc.683C>Gā(p.Thr228Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00102 in 1,614,186 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003793.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00106 AC: 161AN: 152190Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000994 AC: 250AN: 251440Hom.: 2 AF XY: 0.000964 AC XY: 131AN XY: 135904
GnomAD4 exome AF: 0.00101 AC: 1482AN: 1461878Hom.: 5 Cov.: 34 AF XY: 0.00110 AC XY: 798AN XY: 727242
GnomAD4 genome AF: 0.00106 AC: 162AN: 152308Hom.: 1 Cov.: 32 AF XY: 0.000953 AC XY: 71AN XY: 74470
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
CTSF: BS2 -
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
BS1 -
Neuronal ceroid lipofuscinosis 13 Uncertain:1Benign:1
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Inborn genetic diseases Uncertain:1
The p.T228R variant (also known as c.683C>G), located in coding exon 5 of the CTSF gene, results from a C to G substitution at nucleotide position 683. The threonine at codon 228 is replaced by arginine, an amino acid with similar properties. This amino acid position is well conserved through mammals but not in all available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
CTSF-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at