9-22006243-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_004936.4(CDKN2B):āc.161T>Cā(p.Met54Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000218 in 1,605,032 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004936.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152252Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000388 AC: 9AN: 231936Hom.: 0 AF XY: 0.0000703 AC XY: 9AN XY: 127946
GnomAD4 exome AF: 0.0000220 AC: 32AN: 1452662Hom.: 0 Cov.: 31 AF XY: 0.0000373 AC XY: 27AN XY: 723146
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152370Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74514
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.161T>C (p.M54T) alteration is located in exon 2 (coding exon 2) of the CDKN2B gene. This alteration results from a T to C substitution at nucleotide position 161, causing the methionine (M) at amino acid position 54 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at