rs534471786
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001122630.2(CDKN1C):c.291C>T(p.Pro97=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000139 in 1,526,108 control chromosomes in the GnomAD database, including 3 homozygotes. 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. P97P) 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.291C>T | p.Pro97= | synonymous_variant | 2/4 | ENST00000440480.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKN1C | ENST00000440480.8 | c.291C>T | p.Pro97= | synonymous_variant | 2/4 | 1 | NM_001122630.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152100Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000371 AC: 47AN: 126716Hom.: 1 AF XY: 0.000418 AC XY: 29AN XY: 69450
GnomAD4 exome AF: 0.000146 AC: 200AN: 1373900Hom.: 3 Cov.: 31 AF XY: 0.000193 AC XY: 131AN XY: 677528
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74398
ClinVar
Submissions by phenotype
Beckwith-Wiedemann syndrome;C1846009:IMAGe syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 24, 2022 | - - |
Beckwith-Wiedemann syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at