rs747104008
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001122630.2(CDKN1C):c.771C>T(p.Ser257=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000307 in 1,466,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S257S) has been classified as Likely benign.
Frequency
Consequence
NM_001122630.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKN1C | NM_001122630.2 | c.771C>T | p.Ser257= | synonymous_variant | 2/4 | ENST00000440480.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKN1C | ENST00000440480.8 | c.771C>T | p.Ser257= | synonymous_variant | 2/4 | 1 | NM_001122630.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000732 AC: 11AN: 150284Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000674 AC: 9AN: 133486Hom.: 0 AF XY: 0.0000647 AC XY: 5AN XY: 77286
GnomAD4 exome AF: 0.0000258 AC: 34AN: 1316594Hom.: 0 Cov.: 31 AF XY: 0.0000321 AC XY: 21AN XY: 653288
GnomAD4 genome ? AF: 0.0000732 AC: 11AN: 150284Hom.: 0 Cov.: 33 AF XY: 0.0000818 AC XY: 6AN XY: 73378
ClinVar
Submissions by phenotype
Beckwith-Wiedemann syndrome Benign:3
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Jan 18, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | CDKN1C: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at