Variant rs3128624 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004108.3(FCN2):c.215-9A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 1,595,166 control chromosomes in the GnomAD database, including 100,983 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 0.35 ( 9328 hom., cov: 32)

Exomes 𝑓: 0.35 ( 91655 hom. )

Consequence

FCN2
NM_004108.3 intron

Scores

Splicing: ADA: 0.00001236

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.133

Variant links:

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]

FCN2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
FCN2	NM_004108.3 linkuse as main transcript	c.215-9A>G	intron_variant	ENST00000291744.11	NP_004099.2	Q15485-1
FCN2	NM_015837.3 linkuse as main transcript	c.101-9A>G	intron_variant		NP_056652.1	Q15485-2
FCN2	XM_011518392.4 linkuse as main transcript	c.182-9A>G	intron_variant		XP_011516694.1
FCN2	XM_006717015.5 linkuse as main transcript	c.68-9A>G	intron_variant		XP_006717078.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCN2	ENST00000291744.11 linkuse as main transcript	c.215-9A>G		intron_variant		1	NM_004108.3	ENSP00000291744.6		Q15485-1
FCN2	ENST00000350339.3 linkuse as main transcript	c.101-9A>G		intron_variant		5		ENSP00000291741.5		Q15485-2

Frequencies

GnomAD3 genomes

AF:

0.348

AC:

52879

AN:

151868

Hom.:

9318

Cov.:

show subpopulations

Gnomad AFR

AF:

0.333

Gnomad AMI

AF:

0.190

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.465

Gnomad EAS

AF:

0.435

Gnomad SAS

AF:

0.435

Gnomad FIN

AF:

0.372

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.373

GnomAD3 exomes

AF:

0.361

AC:

90600

AN:

250944

Hom.:

16968

AF XY:

0.368

AC XY:

49967

AN XY:

135738

show subpopulations

Gnomad AFR exome

AF:

0.335

Gnomad AMR exome

AF:

0.266

Gnomad ASJ exome

AF:

0.467

Gnomad EAS exome

AF:

0.444

Gnomad SAS exome

AF:

0.435

Gnomad FIN exome

AF:

0.362

Gnomad NFE exome

AF:

0.351

Gnomad OTH exome

AF:

0.363

GnomAD4 exome

AF:

0.350

AC:

505688

AN:

1443180

Hom.:

91655

Cov.:

AF XY:

0.353

AC XY:

253724

AN XY:

718934

show subpopulations

Gnomad4 AFR exome

AF:

0.327

Gnomad4 AMR exome

AF:

0.275

Gnomad4 ASJ exome

AF:

0.467

Gnomad4 EAS exome

AF:

0.407

Gnomad4 SAS exome

AF:

0.428

Gnomad4 FIN exome

AF:

0.368

Gnomad4 NFE exome

AF:

0.341

Gnomad4 OTH exome

AF:

0.369

GnomAD4 genome

AF:

0.348

AC:

52912

AN:

151986

Hom.:

9328

Cov.:

AF XY:

0.348

AC XY:

25887

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.333

Gnomad4 AMR

AF:

0.318

Gnomad4 ASJ

AF:

0.465

Gnomad4 EAS

AF:

0.435

Gnomad4 SAS

AF:

0.436

Gnomad4 FIN

AF:

0.372

Gnomad4 NFE

AF:

0.343

Gnomad4 OTH

AF:

0.378

Alfa

AF:

0.354

Hom.:

9714

Bravo

AF:

0.344

Asia WGS

AF:

0.424

AC:

1473

AN:

3478

EpiCase

AF:

0.357

EpiControl

AF:

0.359

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

9.0

DANN

Benign

0.47

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000012

dbscSNV1_RF

Benign

0.0040

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over