chr2-96651928-G-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001293083.2(FER1L5):c.541G>T(p.Gly181Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 31)
Consequence
FER1L5
NM_001293083.2 missense
NM_001293083.2 missense
Scores
6
4
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 8.62
Genes affected
FER1L5 (HGNC:19044): (fer-1 like family member 5) Predicted to enable calcium ion binding activity and calcium-dependent phospholipid binding activity. Predicted to be involved in several processes, including myeloid cell activation involved in immune response; negative regulation of phagocytosis; and plasma membrane organization. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. Predicted to be active in T-tubule and cytoplasmic vesicle. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.852
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FER1L5 | NM_001293083.2 | c.541G>T | p.Gly181Cys | missense_variant | 7/53 | ENST00000624922.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FER1L5 | ENST00000624922.6 | c.541G>T | p.Gly181Cys | missense_variant | 7/53 | 5 | NM_001293083.2 | P4 | |
FER1L5 | ENST00000623019.5 | c.541G>T | p.Gly181Cys | missense_variant | 7/52 | A2 | |||
FER1L5 | ENST00000505256.6 | n.549G>T | non_coding_transcript_exon_variant | 6/6 | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Benign
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Uncertain
D
PrimateAI
Uncertain
T
Polyphen
1.0
.;D;.
Vest4
0.69, 0.65
MutPred
Loss of MoRF binding (P = 0.0769);Loss of MoRF binding (P = 0.0769);Loss of MoRF binding (P = 0.0769);
MVP
0.56
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.