rs4545169

Variant names:

• chr9-134890095-T-G
• rs4545169
• ENST00000855732.1:c.*2680T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000855732.1(FCN2):​c.*2680T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,156 control chromosomes in the GnomAD database, including 2,581 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 0.17 (2581 hom., cov: 33)
• Consequence: FCN2 ENST00000855732.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000855732.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCN2	ENST00000855732.1		c.*2680T>G		3_prime_UTR	Exon 8 of 8	ENSP00000525791.1

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25118 AN: 152038 Hom.: 2578 Cov.: 33

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0969

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.165 AC: 25156 AN: 152156 Hom.: 2581 Cov.: 33 AF XY: 0.163 AC XY: 12105 AN XY: 74366

African (AFR) AF: 0.299 AC: 12401 AN: 41482

American (AMR) AF: 0.141 AC: 2148 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0432 AC: 150 AN: 3470

East Asian (EAS) AF: 0.180 AC: 930 AN: 5180

South Asian (SAS) AF: 0.117 AC: 564 AN: 4822

European-Finnish (FIN) AF: 0.0969 AC: 1026 AN: 10592

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7584 AN: 68002

Other (OTH) AF: 0.153 AC: 323 AN: 2116

Alfa AF: 0.169 Hom.: 388

Bravo AF: 0.175

Asia WGS AF: 0.160 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs4545169; hg19: chr9-137781941;