chr9-134880265-A-G

Variant names:

• chr9-134880265-A-G
• rs3811140
• XM_011518392.4:c.68-2261A>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.68-2261A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,098 control chromosomes in the GnomAD database, including 1,794 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 0.15 (1794 hom., cov: 32)
• Consequence: FCN2 XM_011518392.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255
• Publications: 17 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCN2	XM_011518392.4	c.68-2261A>G		intron_variant	Intron 1 of 7		XP_011516694.1
FCN2	XM_006717015.5	c.68-3037A>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: 0.145 AC: 22055 AN: 151980 Hom.: 1783 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0436

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0918

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.145 AC: 22112 AN: 152098 Hom.: 1794 Cov.: 32 AF XY: 0.144 AC XY: 10683 AN XY: 74364

African (AFR) AF: 0.223 AC: 9249 AN: 41460

American (AMR) AF: 0.128 AC: 1957 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0436 AC: 151 AN: 3466

East Asian (EAS) AF: 0.181 AC: 932 AN: 5154

South Asian (SAS) AF: 0.161 AC: 774 AN: 4822

European-Finnish (FIN) AF: 0.0918 AC: 973 AN: 10596

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7723 AN: 68002

Other (OTH) AF: 0.140 AC: 296 AN: 2110

Alfa AF: 0.129 Hom.: 455

Bravo AF: 0.152

Asia WGS AF: 0.173 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.81
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs3811140; hg19: chr9-137772111;