9-130904343-G-A

Variant names:

• chr9-130904343-G-A
• rs12552821
• NM_032843.5:c.1127-20C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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: Benign. The variant received -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 VariationId 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.

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.1127-20C>T		intron	N/A	NP_116232.3
	FIBCD1	NM_001145106.2		c.1127-20C>T		intron	N/A	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.1127-20C>T		intron	N/A	ENSP00000361413.4	Q8N539-1
	FIBCD1	ENST00000448616.5	TSL:5	c.1127-20C>T		intron	N/A	ENSP00000414501.1	Q8N539-1
	FIBCD1	ENST00000872083.1		c.1127-20C>T		intron	N/A	ENSP00000542142.1

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

GnomAD2 exomes AF: 0.243 AC: 56609 AN: 233050 AF XY: 0.232

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 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

African (AFR) AF: 0.145 AC: 4794 AN: 33120

American (AMR) AF: 0.432 AC: 18944 AN: 43862

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 2647 AN: 24924

East Asian (EAS) AF: 0.386 AC: 15130 AN: 39238

South Asian (SAS) AF: 0.192 AC: 16019 AN: 83410

European-Finnish (FIN) AF: 0.288 AC: 14399 AN: 50070

Middle Eastern (MID) AF: 0.115 AC: 626 AN: 5444

European-Non Finnish (NFE) AF: 0.182 AC: 200012 AN: 1096456

Other (OTH) AF: 0.190 AC: 11284 AN: 59270

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

African (AFR) AF: 0.152 AC: 6303 AN: 41510

American (AMR) AF: 0.304 AC: 4646 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 368 AN: 3472

East Asian (EAS) AF: 0.358 AC: 1827 AN: 5100

South Asian (SAS) AF: 0.200 AC: 964 AN: 4816

European-Finnish (FIN) AF: 0.287 AC: 3044 AN: 10606

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12416 AN: 67922

Other (OTH) AF: 0.187 AC: 394 AN: 2110

Alfa AF: 0.193 Hom.: 885

Bravo AF: 0.201

Asia WGS AF: 0.270 AC: 934 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.73
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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