rs414884

Positions:

• chr8-17890609-C-T

Variant summary

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

The NM_004467.4(FGL1):​c.-18+4838G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 151,952 control chromosomes in the GnomAD database, including 34,429 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 0.67 (34429 hom., cov: 31)
• Consequence: FGL1 NM_004467.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986

Genes affected

FGL1 (HGNC:3695): (fibrinogen like 1) Fibrinogen-like 1 is a member of the fibrinogen family. This protein is homologous to the carboxy terminus of the fibrinogen beta- and gamma- subunits which contains the four conserved cysteines of fibrinogens and fibrinogen related proteins. However, this protein lacks the platelet-binding site, cross-linking region and a thrombin-sensitive site which are necessary for fibrin clot formation. This protein may play a role in the development of hepatocellular carcinomas. Four alternatively spliced transcript variants encoding the same protein exist for this gene. [provided by RefSeq, Jul 2008]

FGL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGL1	NM_004467.4	c.-18+4838G>A		intron_variant		ENST00000427924.5	NP_004458.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGL1	ENST00000427924.5	c.-18+4838G>A		intron_variant		1	NM_004467.4	ENSP00000401952.1

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101140 AN: 151832 Hom.: 34414 Cov.: 31

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.666 AC: 101187 AN: 151952 Hom.: 34429 Cov.: 31 AF XY: 0.660 AC XY: 49015 AN XY: 74244

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.679

Alfa AF: 0.709 Hom.: 17510

Bravo AF: 0.644

Asia WGS AF: 0.514 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.086

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: rs414884; hg19: chr8-17748118;