X-83873405-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBS2_Supporting
The NM_021118.3(CYLC1):c.697C>T(p.Pro233Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000109 in 1,202,076 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 44 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P233L) has been classified as Uncertain significance.
Frequency
Consequence
NM_021118.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYLC1 | NM_021118.3 | c.697C>T | p.Pro233Ser | missense_variant | Exon 4 of 5 | ENST00000329312.5 | NP_066941.1 | |
CYLC1 | XM_005262086.5 | c.694C>T | p.Pro232Ser | missense_variant | Exon 4 of 5 | XP_005262143.1 | ||
CYLC1 | NM_001271680.2 | c.174+1835C>T | intron_variant | Intron 3 of 3 | NP_001258609.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYLC1 | ENST00000329312.5 | c.697C>T | p.Pro233Ser | missense_variant | Exon 4 of 5 | 1 | NM_021118.3 | ENSP00000331556.4 | ||
CYLC1 | ENST00000621735.4 | c.174+1835C>T | intron_variant | Intron 3 of 3 | 3 | ENSP00000480907.1 |
Frequencies
GnomAD3 genomes AF: 0.000126 AC: 14AN: 110849Hom.: 0 Cov.: 22 AF XY: 0.0000599 AC XY: 2AN XY: 33363
GnomAD3 exomes AF: 0.000286 AC: 50AN: 175068Hom.: 0 AF XY: 0.000278 AC XY: 17AN XY: 61204
GnomAD4 exome AF: 0.000107 AC: 117AN: 1091176Hom.: 0 Cov.: 30 AF XY: 0.000117 AC XY: 42AN XY: 357776
GnomAD4 genome AF: 0.000126 AC: 14AN: 110900Hom.: 0 Cov.: 22 AF XY: 0.0000598 AC XY: 2AN XY: 33424
ClinVar
Submissions by phenotype
not provided Benign:1
CYLC1: BP4, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at