9-134917528-A-G

Variant names:

• chr9-134917528-A-G
• rs2989726
• NM_002003.5:c.103+241T>C

Variant summary

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

The NM_002003.5(FCN1):​c.103+241T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,096 control chromosomes in the GnomAD database, including 5,250 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 0.26 (5250 hom., cov: 32)
• Consequence: FCN1 NM_002003.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002003.5. 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
	FCN1	NM_002003.5	MANE Select	c.103+241T>C		intron	N/A	NP_001994.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCN1	ENST00000371806.4	TSL:1 MANE Select	c.103+241T>C		intron	N/A	ENSP00000360871.3
	FCN1	ENST00000954365.1		c.103+241T>C		intron	N/A	ENSP00000624424.1
	FCN1	ENST00000954366.1		c.103+241T>C		intron	N/A	ENSP00000624425.1

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38997 AN: 151978 Hom.: 5244 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.308

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.257 AC: 39016 AN: 152096 Hom.: 5250 Cov.: 32 AF XY: 0.262 AC XY: 19497 AN XY: 74348

African (AFR) AF: 0.176 AC: 7301 AN: 41508

American (AMR) AF: 0.231 AC: 3533 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1010 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1609 AN: 5172

South Asian (SAS) AF: 0.382 AC: 1837 AN: 4812

European-Finnish (FIN) AF: 0.295 AC: 3117 AN: 10568

Middle Eastern (MID) AF: 0.307 AC: 89 AN: 290

European-Non Finnish (NFE) AF: 0.290 AC: 19724 AN: 67984

Other (OTH) AF: 0.250 AC: 527 AN: 2110

Alfa AF: 0.274 Hom.: 20198

Bravo AF: 0.242

Asia WGS AF: 0.316 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.023
DANN	Benign	0.34
PhyloP100		-2.0
PromoterAI		-0.014	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2989726; hg19: chr9-137809374;