chr12-108517078-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007076.3(FICD):c.106T>G(p.Ser36Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000048 in 1,457,520 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: not found (cov: 32)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
FICD
NM_007076.3 missense
NM_007076.3 missense
Scores
4
15
Clinical Significance
Conservation
PhyloP100: 4.14
Genes affected
FICD (HGNC:18416): (FIC domain protein adenylyltransferase) Enables several functions, including ATP binding activity; Hsp70 protein binding activity; and chaperone binding activity. Involved in protein adenylylation; regulation of IRE1-mediated unfolded protein response; and response to endoplasmic reticulum stress. Is integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.25834686).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FICD | NM_007076.3 | c.106T>G | p.Ser36Ala | missense_variant | 2/3 | ENST00000552695.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FICD | ENST00000552695.6 | c.106T>G | p.Ser36Ala | missense_variant | 2/3 | 1 | NM_007076.3 | P1 | |
FICD | ENST00000361549.2 | c.106T>G | p.Ser36Ala | missense_variant | 2/3 | 1 | |||
FICD | ENST00000552758.1 | c.106T>G | p.Ser36Ala | missense_variant | 2/2 | 2 | |||
FICD | ENST00000549641.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 248016Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134082
GnomAD3 exomes
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248016
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GnomAD4 exome AF: 0.00000480 AC: 7AN: 1457520Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2AN XY: 724808
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
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Cov.:
32
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2
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 | Oct 03, 2022 | The c.106T>G (p.S36A) alteration is located in exon 2 (coding exon 1) of the FICD gene. This alteration results from a T to G substitution at nucleotide position 106, causing the serine (S) at amino acid position 36 to be replaced by an alanine (A). 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
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.;.
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;D;D
REVEL
Uncertain
Sift
Benign
T;D;D
Sift4G
Benign
T;D;D
Polyphen
B;.;.
Vest4
MutPred
Gain of catalytic residue at V33 (P = 0.0118);Gain of catalytic residue at V33 (P = 0.0118);Gain of catalytic residue at V33 (P = 0.0118);
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