15-88626253-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022767.4(AEN):c.44C>T(p.Pro15Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0543 in 1,611,698 control chromosomes in the GnomAD database, including 2,977 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_022767.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AEN | NM_022767.4 | c.44C>T | p.Pro15Leu | missense_variant | 2/4 | ENST00000332810.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AEN | ENST00000332810.4 | c.44C>T | p.Pro15Leu | missense_variant | 2/4 | 1 | NM_022767.4 | P1 | |
AEN | ENST00000557787.1 | n.154C>T | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
AEN | ENST00000559528.1 | c.44C>T | p.Pro15Leu | missense_variant | 2/2 | 2 | |||
AEN | ENST00000558327.1 | n.525C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0719 AC: 10952AN: 152228Hom.: 499 Cov.: 33
GnomAD3 exomes AF: 0.0582 AC: 14440AN: 247938Hom.: 575 AF XY: 0.0603 AC XY: 8103AN XY: 134420
GnomAD4 exome AF: 0.0524 AC: 76512AN: 1459352Hom.: 2472 Cov.: 31 AF XY: 0.0542 AC XY: 39331AN XY: 725796
GnomAD4 genome AF: 0.0721 AC: 10977AN: 152346Hom.: 505 Cov.: 33 AF XY: 0.0727 AC XY: 5419AN XY: 74496
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at