chr2-9374923-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003887.3(ASAP2):c.1725A>T(p.Lys575Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,609,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003887.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASAP2 | NM_003887.3 | c.1725A>T | p.Lys575Asn | missense_variant | 17/28 | ENST00000281419.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASAP2 | ENST00000281419.8 | c.1725A>T | p.Lys575Asn | missense_variant | 17/28 | 1 | NM_003887.3 | P3 | |
ASAP2 | ENST00000315273.4 | c.1725A>T | p.Lys575Asn | missense_variant | 17/27 | 1 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 150974Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 247016Hom.: 0 AF XY: 0.0000225 AC XY: 3AN XY: 133542
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1458208Hom.: 0 Cov.: 34 AF XY: 0.0000193 AC XY: 14AN XY: 725318
GnomAD4 genome AF: 0.0000132 AC: 2AN: 150974Hom.: 0 Cov.: 31 AF XY: 0.0000136 AC XY: 1AN XY: 73706
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 12, 2024 | The c.1725A>T (p.K575N) alteration is located in exon 17 (coding exon 17) of the ASAP2 gene. This alteration results from a A to T substitution at nucleotide position 1725, causing the lysine (K) at amino acid position 575 to be replaced by an asparagine (N). 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