Variant rs1071583 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002003.5(FCN1):c.825A>G(p.Gln275=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 1,613,890 control chromosomes in the GnomAD database, including 339,132 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 0.70 ( 38568 hom., cov: 32)

Exomes 𝑓: 0.64 ( 300564 hom. )

Consequence

FCN1
NM_002003.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.41

Variant links:

Genes affected

FCN1 (HGNC:3623): (ficolin 1) The ficolin family of proteins are 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. The collagen-like and the fibrinogen-like domains are also found separately in other proteins such as complement protein C1q, C-type lectins known as collectins, and tenascins. However, all these proteins recognize different targets, and are functionally distinct. Ficolin 1 encoded by FCN1 is predominantly expressed in the peripheral blood leukocytes, and has been postulated to function as a plasma protein with elastin-binding activity. [provided by RefSeq, Jul 2008]

FCN1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP7

Synonymous conserved (PhyloP=-3.41 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCN1	NM_002003.5 linkuse as main transcript	c.825A>G	p.Gln275=	synonymous_variant	9/9	ENST00000371806.4	NP_001994.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCN1	ENST00000371806.4 linkuse as main transcript	c.825A>G	p.Gln275=	synonymous_variant	9/9	1	NM_002003.5	ENSP00000360871	P1

Frequencies

GnomAD3 genomes

AF:

0.699

AC:

106287

AN:

151982

Hom.:

38522

Cov.:

show subpopulations

Gnomad AFR

AF:

0.898

Gnomad AMI

AF:

0.817

Gnomad AMR

AF:

0.529

Gnomad ASJ

AF:

0.617

Gnomad EAS

AF:

0.489

Gnomad SAS

AF:

0.708

Gnomad FIN

AF:

0.674

Gnomad MID

AF:

0.703

Gnomad NFE

AF:

0.640

Gnomad OTH

AF:

0.653

GnomAD3 exomes

AF:

0.625

AC:

157129

AN:

251484

Hom.:

51247

AF XY:

0.633

AC XY:

86036

AN XY:

135916

show subpopulations

Gnomad AFR exome

AF:

0.912

Gnomad AMR exome

AF:

0.403

Gnomad ASJ exome

AF:

0.614

Gnomad EAS exome

AF:

0.485

Gnomad SAS exome

AF:

0.717

Gnomad FIN exome

AF:

0.666

Gnomad NFE exome

AF:

0.643

Gnomad OTH exome

AF:

0.616

GnomAD4 exome

AF:

0.637

AC:

931227

AN:

1461790

Hom.:

300564

Cov.:

AF XY:

0.640

AC XY:

465480

AN XY:

727208

show subpopulations

Gnomad4 AFR exome

AF:

0.915

Gnomad4 AMR exome

AF:

0.416

Gnomad4 ASJ exome

AF:

0.613

Gnomad4 EAS exome

AF:

0.455

Gnomad4 SAS exome

AF:

0.719

Gnomad4 FIN exome

AF:

0.658

Gnomad4 NFE exome

AF:

0.637

Gnomad4 OTH exome

AF:

0.643

GnomAD4 genome

AF:

0.699

AC:

106380

AN:

152100

Hom.:

38568

Cov.:

AF XY:

0.697

AC XY:

51829

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.898

Gnomad4 AMR

AF:

0.529

Gnomad4 ASJ

AF:

0.617

Gnomad4 EAS

AF:

0.488

Gnomad4 SAS

AF:

0.707

Gnomad4 FIN

AF:

0.674

Gnomad4 NFE

AF:

0.640

Gnomad4 OTH

AF:

0.650

Alfa

AF:

0.647

Hom.:

41995

Bravo

AF:

0.692

Asia WGS

AF:

0.603

AC:

2097

AN:

3478

EpiCase

AF:

0.629

EpiControl

AF:

0.629

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.58

DANN

Benign

0.44

Splicing

Name

Calibrated prediction

Score

Prediction

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