rs62573178

Positions:

• chr9-134887004-G-A
• chr9-134887004-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004108.3(FCN2):​c.695-164G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,236 control chromosomes in the GnomAD database, including 1,946 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 0.14 (1946 hom., cov: 33)
• Consequence: FCN2 NM_004108.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FCN2	NM_004108.3	c.695-164G>A		intron_variant		ENST00000291744.11	NP_004099.2
FCN2	NM_015837.3	c.581-164G>A		intron_variant			NP_056652.1
FCN2	XM_006717015.5	c.548-164G>A		intron_variant			XP_006717078.1
FCN2	XM_011518392.4	c.662-164G>A		intron_variant			XP_011516694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FCN2	ENST00000291744.11	c.695-164G>A		intron_variant		1	NM_004108.3	ENSP00000291744	P1
FCN2	ENST00000350339.3	c.581-164G>A		intron_variant		5		ENSP00000291741

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21806 AN: 152118 Hom.: 1951 Cov.: 33

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.143 AC: 21794 AN: 152236 Hom.: 1946 Cov.: 33 AF XY: 0.142 AC XY: 10593 AN XY: 74436

Gnomad4 AFR AF: 0.0662

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.144

Alfa AF: 0.146 Hom.: 250

Bravo AF: 0.132

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.82
DANN	Benign	0.29

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

Other links and lift over

dbSNP: rs62573178; hg19: chr9-137778850;