chr9-130924234-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_032843.5(FIBCD1):c.712+3G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00427 in 1,586,494 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0036 ( 3 hom., cov: 33)
Exomes 𝑓: 0.0043 ( 15 hom. )
Consequence
FIBCD1
NM_032843.5 splice_donor_region, intron
NM_032843.5 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.0007164
2
Clinical Significance
Conservation
PhyloP100: 0.540
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 Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
?
Variant 9-130924234-C-T is Benign according to our data. Variant chr9-130924234-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2659618.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FIBCD1 | NM_032843.5 | c.712+3G>A | splice_donor_region_variant, intron_variant | ENST00000372338.9 | |||
FIBCD1 | NM_001145106.2 | c.712+3G>A | splice_donor_region_variant, intron_variant | ||||
FIBCD1 | XM_047423989.1 | c.712+3G>A | splice_donor_region_variant, intron_variant | ||||
FIBCD1 | XM_047423990.1 | c.238+3G>A | splice_donor_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FIBCD1 | ENST00000372338.9 | c.712+3G>A | splice_donor_region_variant, intron_variant | 1 | NM_032843.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00365 AC: 555AN: 152108Hom.: 3 Cov.: 33
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GnomAD3 exomes AF: 0.00273 AC: 566AN: 207236Hom.: 1 AF XY: 0.00271 AC XY: 309AN XY: 113828
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GnomAD4 exome AF: 0.00433 AC: 6213AN: 1434268Hom.: 15 Cov.: 32 AF XY: 0.00410 AC XY: 2912AN XY: 710678
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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
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | FIBCD1: BP4, BS2 - |
Computational scores
Source:
Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at