rs7035023

Positions:

• chr9-130922170-T-C
• chr9-130922170-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032843.5(FIBCD1):​c.849+1574A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,156 control chromosomes in the GnomAD database, including 6,050 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (6050 hom., cov: 33)
• Consequence: FIBCD1 NM_032843.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FIBCD1	NM_032843.5	c.849+1574A>G		intron_variant		ENST00000372338.9
FIBCD1	NM_001145106.2	c.849+1574A>G		intron_variant
FIBCD1	XM_047423989.1	c.849+1574A>G		intron_variant
FIBCD1	XM_047423990.1	c.375+1574A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FIBCD1	ENST00000372338.9	c.849+1574A>G		intron_variant		1	NM_032843.5	P1

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40146 AN: 152038 Hom.: 6032 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.245

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.264 AC: 40202 AN: 152156 Hom.: 6050 Cov.: 33 AF XY: 0.269 AC XY: 19986 AN XY: 74382

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.246

Alfa AF: 0.202 Hom.: 4487

Bravo AF: 0.285

Asia WGS AF: 0.403 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.55

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: rs7035023; hg19: chr9-133797557;