chr9-130905335-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_032843.5(FIBCD1):c.1025C>T(p.Thr342Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000998 in 1,614,012 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
Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
FIBCD1
NM_032843.5 missense
NM_032843.5 missense
Scores
2
12
5
Clinical Significance
Conservation
PhyloP100: 7.63
Genes affected
FIBCD1 (HGNC:25922): (fibrinogen C domain containing 1) FIBCD1 is a conserved type II transmembrane endocytic receptor that binds chitin and is located primarily in the intestinal brush border (Schlosser et al., 2009 [PubMed 19710473]).[supplied by OMIM, Apr 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.811
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FIBCD1 | NM_032843.5 | c.1025C>T | p.Thr342Met | missense_variant | 6/7 | ENST00000372338.9 | |
FIBCD1 | NM_001145106.2 | c.1025C>T | p.Thr342Met | missense_variant | 7/8 | ||
FIBCD1 | XM_047423989.1 | c.1025C>T | p.Thr342Met | missense_variant | 7/8 | ||
FIBCD1 | XM_047423990.1 | c.551C>T | p.Thr184Met | missense_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FIBCD1 | ENST00000372338.9 | c.1025C>T | p.Thr342Met | missense_variant | 6/7 | 1 | NM_032843.5 | P1 | |
FIBCD1 | ENST00000448616.5 | c.1025C>T | p.Thr342Met | missense_variant | 7/8 | 5 | P1 | ||
FIBCD1 | ENST00000372337.6 | c.551C>T | p.Thr184Met | missense_variant | 6/7 | 5 | |||
FIBCD1 | ENST00000444139.5 | c.808-1263C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152224Hom.: 0 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000720 AC: 18AN: 250018Hom.: 0 AF XY: 0.0000665 AC XY: 9AN XY: 135426
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GnomAD4 exome AF: 0.000106 AC: 155AN: 1461670Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 88AN XY: 727134
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GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74482
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ExAC
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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 | Dec 20, 2021 | The c.1025C>T (p.T342M) alteration is located in exon 6 (coding exon 6) of the FIBCD1 gene. This alteration results from a C to T substitution at nucleotide position 1025, causing the threonine (T) at amino acid position 342 to be replaced by a methionine (M). 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
Uncertain
T
BayesDel_noAF
Uncertain
Cadd
Uncertain
Dann
Pathogenic
DEOGEN2
Benign
T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;.;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D
REVEL
Uncertain
Sift
Uncertain
D;D;T
Sift4G
Benign
T;T;T
Polyphen
P;P;.
Vest4
MVP
MPC
0.55
ClinPred
D
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