chr6-36684112-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000389.5(CDKN1A):c.11C>T(p.Pro4Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000962 in 1,613,390 control chromosomes in the GnomAD database, including 17 homozygotes. 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 Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Synonymous variant affecting the same amino acid position (i.e. P4P) has been classified as Benign.
Frequency
Consequence
NM_000389.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKN1A | NM_000389.5 | c.11C>T | p.Pro4Leu | missense_variant | 2/3 | ENST00000244741.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKN1A | ENST00000244741.10 | c.11C>T | p.Pro4Leu | missense_variant | 2/3 | 1 | NM_000389.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00556 AC: 847AN: 152222Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00138 AC: 345AN: 249842Hom.: 3 AF XY: 0.00105 AC XY: 142AN XY: 135366
GnomAD4 exome AF: 0.000478 AC: 699AN: 1461050Hom.: 6 Cov.: 32 AF XY: 0.000421 AC XY: 306AN XY: 726866
GnomAD4 genome ? AF: 0.00560 AC: 853AN: 152340Hom.: 11 Cov.: 32 AF XY: 0.00525 AC XY: 391AN XY: 74510
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at