XM_011518392.4:c.68-2306A>G

Variant names:

• chr9-134880220-A-G
• rs3124953
• XM_011518392.4:c.68-2306A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 39 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FCN2	XM_011518392.4	c.68-2306A>G		intron_variant	Intron 1 of 7		XP_011516694.1
FCN2	XM_006717015.5	c.68-3082A>G		intron_variant	Intron 1 of 6		XP_006717078.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.955 AC: 39676 AN: 41560

American (AMR) AF: 0.797 AC: 12178 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2771 AN: 3472

East Asian (EAS) AF: 0.975 AC: 5037 AN: 5164

South Asian (SAS) AF: 0.865 AC: 4175 AN: 4828

European-Finnish (FIN) AF: 0.805 AC: 8530 AN: 10602

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.787 AC: 53479 AN: 67976

Other (OTH) AF: 0.826 AC: 1745 AN: 2112

Alfa AF: 0.811 Hom.: 16169

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
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs3124953; hg19: chr9-137772066;