9-21994197-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP7BS2_Supporting
The NM_058195.4(CDKN2A):c.135C>A(p.Leu45Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000344 in 1,454,200 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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. L45L) has been classified as Likely benign.
Frequency
Consequence
NM_058195.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDKN2A | NM_058195.4 | c.135C>A | p.Leu45Leu | synonymous_variant | Exon 1 of 3 | ENST00000579755.2 | NP_478102.2 | |
CDKN2A | NM_001363763.2 | c.-4+624C>A | intron_variant | Intron 1 of 2 | NP_001350692.1 | |||
CDKN2A | XM_047422597.1 | c.-4+350C>A | intron_variant | Intron 1 of 2 | XP_047278553.1 | |||
LOC124902130 | XR_007061436.1 | n.-169C>A | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1454200Hom.: 0 Cov.: 32 AF XY: 0.00000414 AC XY: 3AN XY: 723780
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Familial melanoma Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at