rs7037264

Variant names:

• chr9-134883366-G-A
• rs7037264
• NM_004108.3:c.268+11G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-134883366-G-A
• chr9-134883366-G-C

Variant summary

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

The NM_004108.3(FCN2):​c.268+11G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 1,610,220 control chromosomes in the GnomAD database, including 142,686 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 0.47 (17874 hom., cov: 30)
  • Exomes 𝑓: 0.41 (124812 hom.)
• Consequence: FCN2 NM_004108.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 18 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004108.3. 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
	FCN2	NM_004108.3	MANE Select	c.268+11G>A		intron	N/A	NP_004099.2	Q15485-1
	FCN2	NM_015837.3		c.154+11G>A		intron	N/A	NP_056652.1	Q15485-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCN2	ENST00000291744.11	TSL:1 MANE Select	c.268+11G>A		intron	N/A	ENSP00000291744.6	Q15485-1
	FCN2	ENST00000855732.1		c.279G>A	p.Gly93Gly	synonymous	Exon 3 of 8	ENSP00000525791.1
	FCN2	ENST00000855735.1		c.279G>A	p.Gly93Gly	synonymous	Exon 3 of 8	ENSP00000525794.1

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72040 AN: 151770 Hom.: 17830 Cov.: 30

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.434

GnomAD2 exomes AF: 0.431 AC: 107838 AN: 250132 AF XY: 0.422

Gnomad AFR exome AF: 0.625

Gnomad AMR exome AF: 0.470

Gnomad ASJ exome AF: 0.314

Gnomad EAS exome AF: 0.531

Gnomad FIN exome AF: 0.404

Gnomad NFE exome AF: 0.401

Gnomad OTH exome AF: 0.407

GnomAD4 exome AF: 0.410 AC: 598023 AN: 1458334 Hom.: 124812 Cov.: 33 AF XY: 0.409 AC XY: 296828 AN XY: 725688

African (AFR) AF: 0.622 AC: 20742 AN: 33352

American (AMR) AF: 0.471 AC: 21045 AN: 44702

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 7974 AN: 26108

East Asian (EAS) AF: 0.548 AC: 21752 AN: 39686

South Asian (SAS) AF: 0.397 AC: 34216 AN: 86186

European-Finnish (FIN) AF: 0.399 AC: 21257 AN: 53312

Middle Eastern (MID) AF: 0.367 AC: 2113 AN: 5758

European-Non Finnish (NFE) AF: 0.401 AC: 444151 AN: 1108970

Other (OTH) AF: 0.411 AC: 24773 AN: 60260

GnomAD4 genome AF: 0.475 AC: 72139 AN: 151886 Hom.: 17874 Cov.: 30 AF XY: 0.475 AC XY: 35223 AN XY: 74212

African (AFR) AF: 0.623 AC: 25807 AN: 41420

American (AMR) AF: 0.467 AC: 7133 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1072 AN: 3466

East Asian (EAS) AF: 0.539 AC: 2755 AN: 5108

South Asian (SAS) AF: 0.403 AC: 1934 AN: 4798

European-Finnish (FIN) AF: 0.403 AC: 4258 AN: 10556

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27588 AN: 67936

Other (OTH) AF: 0.431 AC: 908 AN: 2106

Alfa AF: 0.426 Hom.: 11000

Bravo AF: 0.484

Asia WGS AF: 0.479 AC: 1668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.73
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7037264; hg19: chr9-137775212; COSMIC: COSV52475894;