13-30255589-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032116.5(KATNAL1):āc.350A>Gā(p.Asn117Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000825 in 1,539,370 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_032116.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KATNAL1 | NM_032116.5 | c.350A>G | p.Asn117Ser | missense_variant | 4/11 | ENST00000380615.8 | NP_115492.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KATNAL1 | ENST00000380615.8 | c.350A>G | p.Asn117Ser | missense_variant | 4/11 | 1 | NM_032116.5 | ENSP00000369989 | P1 | |
KATNAL1 | ENST00000380617.7 | c.350A>G | p.Asn117Ser | missense_variant | 4/11 | 2 | ENSP00000369991 | P1 | ||
KATNAL1 | ENST00000414289.5 | c.350A>G | p.Asn117Ser | missense_variant | 4/4 | 4 | ENSP00000397776 | |||
KATNAL1 | ENST00000441394.1 | c.350A>G | p.Asn117Ser | missense_variant | 4/4 | 3 | ENSP00000407792 |
Frequencies
GnomAD3 genomes AF: 0.000282 AC: 41AN: 145176Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000850 AC: 18AN: 211740Hom.: 0 AF XY: 0.0000775 AC XY: 9AN XY: 116112
GnomAD4 exome AF: 0.0000624 AC: 87AN: 1394094Hom.: 0 Cov.: 31 AF XY: 0.0000722 AC XY: 50AN XY: 692754
GnomAD4 genome AF: 0.000275 AC: 40AN: 145276Hom.: 0 Cov.: 30 AF XY: 0.000286 AC XY: 20AN XY: 69932
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 07, 2022 | The c.350A>G (p.N117S) alteration is located in exon 4 (coding exon 3) of the KATNAL1 gene. This alteration results from a A to G substitution at nucleotide position 350, causing the asparagine (N) at amino acid position 117 to be replaced by a serine (S). 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