19-41220710-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_021913.5(AXL):c.160C>A(p.Leu54Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,412 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021913.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AXL | ENST00000301178.9 | c.160C>A | p.Leu54Ile | missense_variant | Exon 2 of 20 | 1 | NM_021913.5 | ENSP00000301178.3 | ||
AXL | ENST00000359092.7 | c.160C>A | p.Leu54Ile | missense_variant | Exon 2 of 19 | 1 | ENSP00000351995.2 | |||
AXL | ENST00000599659.5 | n.174C>A | non_coding_transcript_exon_variant | Exon 2 of 12 | 1 | |||||
AXL | ENST00000594880.1 | n.177C>A | non_coding_transcript_exon_variant | Exon 2 of 4 | 4 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249740Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135056
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461412Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726938
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.160C>A (p.L54I) alteration is located in exon 2 (coding exon 2) of the AXL gene. This alteration results from a C to A substitution at nucleotide position 160, causing the leucine (L) at amino acid position 54 to be replaced by an isoleucine (I). 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