9-130904343-G-A

Position:

• chr9-130904343-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_032843.5(FIBCD1):​c.1127-20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 1,587,832 control chromosomes in the GnomAD database, including 34,689 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.20 (3369 hom., cov: 33)
  • Exomes 𝑓: 0.20 (31320 hom.)
• Consequence: FIBCD1 NM_032843.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.204

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

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 9-130904343-G-A is Benign according to our data. Variant chr9-130904343-G-A is described in ClinVar as [Benign]. Clinvar id is 1237806.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FIBCD1	NM_032843.5	c.1127-20C>T		intron_variant		ENST00000372338.9	NP_116232.3
FIBCD1	NM_001145106.2	c.1127-20C>T		intron_variant			NP_001138578.1
FIBCD1	XM_047423989.1	c.1127-20C>T		intron_variant			XP_047279945.1
FIBCD1	XM_047423990.1	c.653-20C>T		intron_variant			XP_047279946.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FIBCD1	ENST00000372338.9	c.1127-20C>T		intron_variant		1	NM_032843.5	ENSP00000361413.4
FIBCD1	ENST00000448616.5	c.1127-20C>T		intron_variant		5		ENSP00000414501.1
FIBCD1	ENST00000444139.5	c.806-271C>T		intron_variant		2		ENSP00000395319.1
FIBCD1	ENST00000372337.6	c.653-20C>T		intron_variant		5		ENSP00000361412.1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30067 AN: 151920 Hom.: 3352 Cov.: 33

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.187

GnomAD3 exomes AF: 0.243 AC: 56609 AN: 233050 Hom.: 8374 AF XY: 0.232 AC XY: 29223 AN XY: 126092

Gnomad AFR exome AF: 0.151

Gnomad AMR exome AF: 0.446

Gnomad ASJ exome AF: 0.112

Gnomad EAS exome AF: 0.342

Gnomad SAS exome AF: 0.198

Gnomad FIN exome AF: 0.295

Gnomad NFE exome AF: 0.188

Gnomad OTH exome AF: 0.214

GnomAD4 exome AF: 0.198 AC: 283855 AN: 1435794 Hom.: 31320 Cov.: 37 AF XY: 0.196 AC XY: 139175 AN XY: 709888

Gnomad4 AFR exome AF: 0.145

Gnomad4 AMR exome AF: 0.432

Gnomad4 ASJ exome AF: 0.106

Gnomad4 EAS exome AF: 0.386

Gnomad4 SAS exome AF: 0.192

Gnomad4 FIN exome AF: 0.288

Gnomad4 NFE exome AF: 0.182

Gnomad4 OTH exome AF: 0.190

GnomAD4 genome AF: 0.198 AC: 30100 AN: 152038 Hom.: 3369 Cov.: 33 AF XY: 0.204 AC XY: 15163 AN XY: 74288

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.187

Alfa AF: 0.188 Hom.: 558

Bravo AF: 0.201

Asia WGS AF: 0.270 AC: 934 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 04, 2020	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12552821; hg19: chr9-133779730; COSMIC: COSV53393770;