XM_011518392.4:c.68-2690A>G

Variant names:

• chr9-134879836-A-G
• rs3124952
• XM_011518392.4:c.68-2690A>G

Variant summary

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

The XM_011518392.4(FCN2):​c.68-2690A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,006 control chromosomes in the GnomAD database, including 26,841 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 0.58 (26841 hom., cov: 32)
• Consequence: FCN2 XM_011518392.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

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=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCN2	XM_011518392.4	c.68-2690A>G		intron_variant	Intron 1 of 7		XP_011516694.1
FCN2	XM_006717015.5	c.68-3466A>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: 0.578 AC: 87725 AN: 151888 Hom.: 26779 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.578 AC: 87852 AN: 152006 Hom.: 26841 Cov.: 32 AF XY: 0.580 AC XY: 43063 AN XY: 74284

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.576

Alfa AF: 0.497 Hom.: 18987

Bravo AF: 0.592

Asia WGS AF: 0.754 AC: 2624 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	0.011
DANN	Benign	0.095

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3124952; hg19: chr9-137771682;