Variant rs10858293 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.33G>T(p.Gly11=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 1,612,054 control chromosomes in the GnomAD database, including 82,141 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 0.31 ( 7564 hom., cov: 32)

Exomes 𝑓: 0.31 ( 74577 hom. )

Consequence

FCN1
NM_002003.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.99

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=-0.86).

BP7

Synonymous conserved (PhyloP=-1.99 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 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.33G>T	p.Gly11=	synonymous_variant	1/9	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.33G>T	p.Gly11=	synonymous_variant	1/9	1	NM_002003.5	ENSP00000360871	P1

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47436

AN:

151874

Hom.:

7560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.313

Gnomad AMI

AF:

0.502

Gnomad AMR

AF:

0.245

Gnomad ASJ

AF:

0.335

Gnomad EAS

AF:

0.120

Gnomad SAS

AF:

0.207

Gnomad FIN

AF:

0.361

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.338

Gnomad OTH

AF:

0.303

GnomAD3 exomes

AF:

0.281

AC:

70571

AN:

251088

Hom.:

10851

AF XY:

0.283

AC XY:

38470

AN XY:

135728

show subpopulations

Gnomad AFR exome

AF:

0.318

Gnomad AMR exome

AF:

0.163

Gnomad ASJ exome

AF:

0.328

Gnomad EAS exome

AF:

0.112

Gnomad SAS exome

AF:

0.215

Gnomad FIN exome

AF:

0.352

Gnomad NFE exome

AF:

0.338

Gnomad OTH exome

AF:

0.295

GnomAD4 exome

AF:

0.314

AC:

459169

AN:

1460062

Hom.:

74577

Cov.:

AF XY:

0.313

AC XY:

227123

AN XY:

726434

show subpopulations

Gnomad4 AFR exome

AF:

0.316

Gnomad4 AMR exome

AF:

0.171

Gnomad4 ASJ exome

AF:

0.330

Gnomad4 EAS exome

AF:

0.112

Gnomad4 SAS exome

AF:

0.221

Gnomad4 FIN exome

AF:

0.340

Gnomad4 NFE exome

AF:

0.334

Gnomad4 OTH exome

AF:

0.303

GnomAD4 genome

AF:

0.312

AC:

47449

AN:

151992

Hom.:

7564

Cov.:

AF XY:

0.309

AC XY:

22920

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.313

Gnomad4 AMR

AF:

0.245

Gnomad4 ASJ

AF:

0.335

Gnomad4 EAS

AF:

0.119

Gnomad4 SAS

AF:

0.206

Gnomad4 FIN

AF:

0.361

Gnomad4 NFE

AF:

0.338

Gnomad4 OTH

AF:

0.299

Alfa

AF:

0.315

Hom.:

10081

Bravo

AF:

0.305

Asia WGS

AF:

0.166

AC:

580

AN:

3478

EpiCase

AF:

0.333

EpiControl

AF:

0.337

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.22

DANN

Benign

0.38

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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