chr9-134881650-C-T

Variant summary

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

The NM_004108.3(FCN2):​c.100+729C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,982 control chromosomes in the GnomAD database, including 8,233 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 0.32 ( 8233 hom., cov: 32)

Consequence

FCN2
NM_004108.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.130
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]

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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=-0.95).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FCN2NM_004108.3 linkuse as main transcriptc.100+729C>T intron_variant ENST00000291744.11
FCN2NM_015837.3 linkuse as main transcriptc.100+729C>T intron_variant
FCN2XM_006717015.5 linkuse as main transcriptc.68-1652C>T intron_variant
FCN2XM_011518392.4 linkuse as main transcriptc.68-876C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FCN2ENST00000291744.11 linkuse as main transcriptc.100+729C>T intron_variant 1 NM_004108.3 P1Q15485-1
FCN2ENST00000350339.3 linkuse as main transcriptc.100+729C>T intron_variant 5 Q15485-2

Frequencies

GnomAD3 genomes
AF:
0.322
AC:
48871
AN:
151864
Hom.:
8229
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.217
Gnomad AMI
AF:
0.230
Gnomad AMR
AF:
0.308
Gnomad ASJ
AF:
0.442
Gnomad EAS
AF:
0.332
Gnomad SAS
AF:
0.428
Gnomad FIN
AF:
0.378
Gnomad MID
AF:
0.396
Gnomad NFE
AF:
0.365
Gnomad OTH
AF:
0.349
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.322
AC:
48882
AN:
151982
Hom.:
8233
Cov.:
32
AF XY:
0.322
AC XY:
23887
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.217
Gnomad4 AMR
AF:
0.308
Gnomad4 ASJ
AF:
0.442
Gnomad4 EAS
AF:
0.331
Gnomad4 SAS
AF:
0.428
Gnomad4 FIN
AF:
0.378
Gnomad4 NFE
AF:
0.365
Gnomad4 OTH
AF:
0.352
Alfa
AF:
0.343
Hom.:
3827
Bravo
AF:
0.312
Asia WGS
AF:
0.376
AC:
1306
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.2
DANN
Benign
0.54

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.

Other links and lift over

dbSNP: rs3124954; hg19: chr9-137773496; API