chr3-124562997-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BS2
The NM_001388419.1(KALRN):c.5090C>T(p.Pro1697Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000263 in 1,367,778 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1697Q) has been classified as Benign.
Frequency
Consequence
NM_001388419.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KALRN | NM_001388419.1 | c.5090C>T | p.Pro1697Leu | missense_variant | 34/60 | ENST00000682506.1 | |
LOC105374076 | XR_001740872.2 | n.187-7776G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KALRN | ENST00000682506.1 | c.5090C>T | p.Pro1697Leu | missense_variant | 34/60 | NM_001388419.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 248840Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135190
GnomAD4 exome AF: 0.0000230 AC: 28AN: 1215576Hom.: 0 Cov.: 30 AF XY: 0.0000216 AC XY: 13AN XY: 602448
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74342
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at