chr9-134880220-A-G

Position:

• chr9-134880220-A-G

Variant summary

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

The XM_011518392.4(FCN2):​c.68-2306A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 152,204 control chromosomes in the GnomAD database, including 54,780 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 0.85 (54780 hom., cov: 31)
• Consequence: FCN2 XM_011518392.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

Genes affected

FCN2 (HGNC:3624): (ficolin 2) The product of this gene belongs to the ficolin family of proteins. This family is characterized by the presence of a leader peptide, a short N-terminal segment, followed by a collagen-like region, and a C-terminal fibrinogen-like domain. This gene is predominantly expressed in the liver, and has been shown to have carbohydrate binding and opsonic activities. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCN2	XM_011518392.4	c.68-2306A>G		intron_variant			XP_011516694.1
FCN2	XM_006717015.5	c.68-3082A>G		intron_variant			XP_006717078.1
		n.134880220A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128499 AN: 152086 Hom.: 54721 Cov.: 31

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.845 AC: 128619 AN: 152204 Hom.: 54780 Cov.: 31 AF XY: 0.845 AC XY: 62894 AN XY: 74410

Gnomad4 AFR AF: 0.955

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.975

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.826

Alfa AF: 0.792 Hom.: 7499

Bravo AF: 0.848

Asia WGS AF: 0.913 AC: 3175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3124953; hg19: chr9-137772066;