19-41220661-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_021913.5(AXL):c.111C>T(p.Phe37Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000138 in 1,595,986 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000010 ( 0 hom. )
Consequence
AXL
NM_021913.5 synonymous
NM_021913.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.28
Genes affected
AXL (HGNC:905): (AXL receptor tyrosine kinase) The protein encoded by this gene is a member of the Tyro3-Axl-Mer (TAM) receptor tyrosine kinase subfamily. The encoded protein possesses an extracellular domain which is composed of two immunoglobulin-like motifs at the N-terminal, followed by two fibronectin type-III motifs. It transduces signals from the extracellular matrix into the cytoplasm by binding to the vitamin K-dependent protein growth arrest-specific 6 (Gas6). This gene may be involved in several cellular functions including growth, migration, aggregation and anti-inflammation in multiple cell types. The encoded protein acts as a host cell receptor for multiple viruses, including Marburg, Ebola and Lassa viruses and is a candidate receptor for the SARS-CoV2 virus. [provided by RefSeq, Sep 2021]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 19-41220661-C-T is Benign according to our data. Variant chr19-41220661-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3610158.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.28 with no splicing effect.
BS2
High AC in GnomAd4 at 7 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AXL | ENST00000301178.9 | c.111C>T | p.Phe37Phe | synonymous_variant | Exon 2 of 20 | 1 | NM_021913.5 | ENSP00000301178.3 | ||
AXL | ENST00000359092.7 | c.111C>T | p.Phe37Phe | synonymous_variant | Exon 2 of 19 | 1 | ENSP00000351995.2 | |||
AXL | ENST00000599659.5 | n.125C>T | non_coding_transcript_exon_variant | Exon 2 of 12 | 1 | |||||
AXL | ENST00000594880.1 | n.128C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152202Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000228 AC: 5AN: 219456Hom.: 0 AF XY: 0.0000336 AC XY: 4AN XY: 118908
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GnomAD4 exome AF: 0.0000104 AC: 15AN: 1443784Hom.: 0 Cov.: 31 AF XY: 0.0000126 AC XY: 9AN XY: 716980
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GnomAD4 genome AF: 0.0000460 AC: 7AN: 152202Hom.: 0 Cov.: 31 AF XY: 0.0000672 AC XY: 5AN XY: 74356
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 19, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at