rs62573178

Variant names:

• chr9-134887004-G-A
• rs62573178
• NM_004108.3:c.695-164G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.187 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCN2	NM_004108.3	MANE Select	c.695-164G>A		intron	N/A	NP_004099.2
	FCN2	NM_015837.3		c.581-164G>A		intron	N/A	NP_056652.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FCN2	ENST00000291744.11	TSL:1 MANE Select	c.695-164G>A		intron	N/A	ENSP00000291744.6
	FCN2	ENST00000350339.3	TSL:5	c.581-164G>A		intron	N/A	ENSP00000291741.5

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

African (AFR) AF: 0.0662 AC: 2751 AN: 41530

American (AMR) AF: 0.121 AC: 1853 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3472

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5178

South Asian (SAS) AF: 0.131 AC: 631 AN: 4826

European-Finnish (FIN) AF: 0.209 AC: 2219 AN: 10596

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12910 AN: 68016

Other (OTH) AF: 0.144 AC: 304 AN: 2110

Alfa AF: 0.150 Hom.: 590

Bravo AF: 0.132

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.82
DANN	Benign	0.29
PhyloP100		-0.50
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: rs62573178; hg19: chr9-137778850;