chr5-36153033-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005983.4(SKP2):āc.271A>Gā(p.Asn91Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000644 in 1,613,772 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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. N91K) has been classified as Uncertain significance.
Frequency
Consequence
NM_005983.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SKP2 | NM_005983.4 | c.271A>G | p.Asn91Asp | missense_variant | 2/10 | ENST00000274255.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SKP2 | ENST00000274255.11 | c.271A>G | p.Asn91Asp | missense_variant | 2/10 | 1 | NM_005983.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249820Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135424
GnomAD4 exome AF: 0.0000629 AC: 92AN: 1461614Hom.: 0 Cov.: 31 AF XY: 0.0000619 AC XY: 45AN XY: 727044
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2024 | The c.271A>G (p.N91D) alteration is located in exon 2 (coding exon 2) of the SKP2 gene. This alteration results from a A to G substitution at nucleotide position 271, causing the asparagine (N) at amino acid position 91 to be replaced by an aspartic acid (D). 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