9-134884208-G-A

Position:

• chr9-134884208-G-A

Variant summary

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

The NM_004108.3(FCN2):​c.269-532G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,924 control chromosomes in the GnomAD database, including 17,215 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 0.47 (17215 hom., cov: 31)
• Consequence: FCN2 NM_004108.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCN2	NM_004108.3	c.269-532G>A		intron_variant		ENST00000291744.11	NP_004099.2
FCN2	NM_015837.3	c.155-532G>A		intron_variant			NP_056652.1
FCN2	XM_011518392.4	c.236-532G>A		intron_variant			XP_011516694.1
FCN2	XM_006717015.5	c.122-532G>A		intron_variant			XP_006717078.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCN2	ENST00000291744.11	c.269-532G>A		intron_variant		1	NM_004108.3	ENSP00000291744.6
FCN2	ENST00000350339.3	c.155-532G>A		intron_variant		5		ENSP00000291741.5

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71978 AN: 151806 Hom.: 17198 Cov.: 31

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.474 AC: 72033 AN: 151924 Hom.: 17215 Cov.: 31 AF XY: 0.473 AC XY: 35100 AN XY: 74258

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.501

Alfa AF: 0.470 Hom.: 4654

Bravo AF: 0.475

Asia WGS AF: 0.571 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.62

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: rs7041446; hg19: chr9-137776054;