chr5-108954928-T-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005246.4(FER):c.1529T>G(p.Val510Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000043 in 1,603,272 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 Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000045 ( 0 hom. )
Consequence
FER
NM_005246.4 missense
NM_005246.4 missense
Scores
7
12
Clinical Significance
Conservation
PhyloP100: 5.03
Genes affected
FER (HGNC:3655): (FER tyrosine kinase) The protein encoded by this gene is a member of the FPS/FES family of non-transmembrane receptor tyrosine kinases. It regulates cell-cell adhesion and mediates signaling from the cell surface to the cytoskeleton via growth factor receptors. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome X. [provided by RefSeq, Apr 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.18232685).
BS2
?
High AC in GnomAdExome at 11 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FER | NM_005246.4 | c.1529T>G | p.Val510Gly | missense_variant | 12/20 | ENST00000281092.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FER | ENST00000281092.9 | c.1529T>G | p.Val510Gly | missense_variant | 12/20 | 1 | NM_005246.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 151966Hom.: 0 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0000445 AC: 11AN: 247292Hom.: 0 AF XY: 0.0000374 AC XY: 5AN XY: 133830
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GnomAD4 exome AF: 0.0000448 AC: 65AN: 1451306Hom.: 0 Cov.: 30 AF XY: 0.0000471 AC XY: 34AN XY: 721776
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 151966Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74230
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2023 | The c.1529T>G (p.V510G) alteration is located in exon 12 (coding exon 10) of the FER gene. This alteration results from a T to G substitution at nucleotide position 1529, causing the valine (V) at amino acid position 510 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;.
REVEL
Uncertain
Sift
Uncertain
D;.;.
Sift4G
Uncertain
D;T;T
Polyphen
B;.;.
Vest4
MutPred
Loss of stability (P = 0.0064);.;.;
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at