9-130905255-C-T

Variant names:

• chr9-130905255-C-T
• rs1303047877
• NM_032843.5:c.1105G>A

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_032843.5(FIBCD1):​c.1105G>A​(p.Ala369Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: FIBCD1 NM_032843.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.89
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2705067).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032843.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FIBCD1	NM_032843.5	MANE Select	c.1105G>A	p.Ala369Thr	missense	Exon 6 of 7	NP_116232.3
	FIBCD1	NM_001145106.2		c.1105G>A	p.Ala369Thr	missense	Exon 7 of 8	NP_001138578.1	Q8N539-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FIBCD1	ENST00000372338.9	TSL:1 MANE Select	c.1105G>A	p.Ala369Thr	missense	Exon 6 of 7	ENSP00000361413.4	Q8N539-1
	FIBCD1	ENST00000448616.5	TSL:5	c.1105G>A	p.Ala369Thr	missense	Exon 7 of 8	ENSP00000414501.1	Q8N539-1
	FIBCD1	ENST00000872083.1		c.1105G>A	p.Ala369Thr	missense	Exon 7 of 8	ENSP00000542142.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.069
BayesDel_addAF	Benign	-0.017	T
BayesDel_noAF	Benign	-0.26
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.022	T
Eigen	Benign	-0.092
Eigen_PC	Benign	0.069
FATHMM_MKL	Uncertain	0.79	D
LIST_S2	Uncertain	0.90	D
M_CAP	Uncertain	0.093	D
MetaRNN	Benign	0.27	T
MetaSVM	Benign	-0.37	T
MutationAssessor	Benign	0.15	N
PhyloP100		1.9
PrimateAI	Uncertain	0.63	T
PROVEAN	Benign	-1.1	N
REVEL	Uncertain	0.34
Sift	Uncertain	0.029	D
Sift4G	Uncertain	0.045	D
Polyphen		0.0010	B
Vest4		0.14
MutPred		0.58		Loss of helix (P = 0.0558)
MVP		0.78
MPC		0.12
ClinPred		0.67	D
GERP RS		4.1
Varity_R		0.25
gMVP		0.51
Mutation Taster		=57/43	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1303047877; hg19: chr9-133780642; COSMIC: COSV53392736;