9-130904061-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_032843.5(FIBCD1):c.*3T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 1,610,990 control chromosomes in the GnomAD database, including 47,977 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.25 (4788 hom., cov: 33)
  • Exomes 𝑓: 0.24 (43189 hom.)
• Consequence: FIBCD1 NM_032843.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.44

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 9-130904061-A-G is Benign according to our data. Variant chr9-130904061-A-G is described in ClinVar as [Benign]. Clinvar id is 1288850.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FIBCD1	NM_032843.5	c.*3T>C		3_prime_UTR_variant	7/7	ENST00000372338.9
FIBCD1	NM_001145106.2	c.*3T>C		3_prime_UTR_variant	8/8
FIBCD1	XM_047423989.1	c.*3T>C		3_prime_UTR_variant	8/8
FIBCD1	XM_047423990.1	c.*3T>C		3_prime_UTR_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FIBCD1	ENST00000372338.9	c.*3T>C		3_prime_UTR_variant	7/7	1	NM_032843.5	P1
FIBCD1	ENST00000444139.5	c.820T>C	p.Trp274Arg	missense_variant	5/5	2
FIBCD1	ENST00000372337.6	c.*3T>C		3_prime_UTR_variant	7/7	5
FIBCD1	ENST00000448616.5	c.*3T>C		3_prime_UTR_variant	8/8	5		P1

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37733 AN: 151928 Hom.: 4780 Cov.: 33

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.238

GnomAD3 exomes AF: 0.237 AC: 58000 AN: 244530 Hom.: 6981 AF XY: 0.240 AC XY: 32040 AN XY: 133382

Gnomad AFR exome AF: 0.272

Gnomad AMR exome AF: 0.212

Gnomad ASJ exome AF: 0.270

Gnomad EAS exome AF: 0.186

Gnomad SAS exome AF: 0.280

Gnomad FIN exome AF: 0.204

Gnomad NFE exome AF: 0.240

Gnomad OTH exome AF: 0.245

GnomAD4 exome AF: 0.242 AC: 353302 AN: 1458946 Hom.: 43189 Cov.: 34 AF XY: 0.243 AC XY: 176594 AN XY: 725722

Gnomad4 AFR exome AF: 0.280

Gnomad4 AMR exome AF: 0.214

Gnomad4 ASJ exome AF: 0.265

Gnomad4 EAS exome AF: 0.178

Gnomad4 SAS exome AF: 0.278

Gnomad4 FIN exome AF: 0.208

Gnomad4 NFE exome AF: 0.242

Gnomad4 OTH exome AF: 0.251

GnomAD4 genome AF: 0.248 AC: 37770 AN: 152044 Hom.: 4788 Cov.: 33 AF XY: 0.248 AC XY: 18394 AN XY: 74318

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.243

Alfa AF: 0.244 Hom.: 6657

Bravo AF: 0.249

Asia WGS AF: 0.262 AC: 910 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

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	-0.87
Cadd	Benign	0.040
Dann	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs11792889; hg19: chr9-133779448; COSMIC: COSV53394050;