14-24573779-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001911.3(CTSG):āc.626A>Gā(p.Asn209Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,614,028 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001911.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTSG | NM_001911.3 | c.626A>G | p.Asn209Ser | missense_variant | 5/5 | ENST00000216336.3 | |
CTSG | XM_011536499.2 | c.668A>G | p.Asn223Ser | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTSG | ENST00000216336.3 | c.626A>G | p.Asn209Ser | missense_variant | 5/5 | 1 | NM_001911.3 | P1 | |
CTSG | ENST00000552252.1 | n.1107A>G | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152060Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250848Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135642
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461850Hom.: 2 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 727230
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152178Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 07, 2022 | The c.626A>G (p.N209S) alteration is located in exon 5 (coding exon 5) of the CTSG gene. This alteration results from a A to G substitution at nucleotide position 626, causing the asparagine (N) at amino acid position 209 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at