chr5-134411725-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_080656.3(CDKN2AIPNL):āc.130A>Gā(p.Ile44Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000459 in 1,613,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I44L) has been classified as Uncertain significance.
Frequency
Consequence
NM_080656.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKN2AIPNL | NM_080656.3 | c.130A>G | p.Ile44Val | missense_variant | 1/3 | ENST00000458198.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKN2AIPNL | ENST00000458198.3 | c.130A>G | p.Ile44Val | missense_variant | 1/3 | 1 | NM_080656.3 | P1 | |
CDKN2AIPNL | ENST00000395009.3 | c.130A>G | p.Ile44Val | missense_variant | 1/2 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247436Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134574
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1460924Hom.: 0 Cov.: 32 AF XY: 0.0000427 AC XY: 31AN XY: 726756
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 08, 2023 | The c.130A>G (p.I44V) alteration is located in exon 1 (coding exon 1) of the CDKN2AIPNL gene. This alteration results from a A to G substitution at nucleotide position 130, causing the isoleucine (I) at amino acid position 44 to be replaced by a valine (V). 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