4-154606284-C-T

Position:

• chr4-154606284-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_021870.3(FGG):​c.1129+421G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,050 control chromosomes in the GnomAD database, including 5,495 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.26 (5495 hom., cov: 32)
• Consequence: FGG NM_021870.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.24

Genes affected

FGG (HGNC:3694): (fibrinogen gamma chain) The protein encoded by this gene is the gamma component of fibrinogen, a blood-borne glycoprotein comprised of three pairs of nonidentical polypeptide chains. Following vascular injury, fibrinogen is cleaved by thrombin to form fibrin which is the most abundant component of blood clots. In addition, various cleavage products of fibrinogen and fibrin regulate cell adhesion and spreading, display vasoconstrictor and chemotactic activities, and are mitogens for several cell types. Mutations in this gene lead to several disorders, including dysfibrinogenemia, hypofibrinogenemia and thrombophilia. Alternative splicing results in transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 4-154606284-C-T is Benign according to our data. Variant chr4-154606284-C-T is described in ClinVar as [Benign]. Clinvar id is 1234766.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FGG	NM_021870.3	c.1129+421G>A		intron_variant		ENST00000336098.8
FGG	NM_000509.6	c.1129+421G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGG	ENST00000336098.8	c.1129+421G>A		intron_variant		2	NM_021870.3

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39903 AN: 151932 Hom.: 5488 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.263 AC: 39941 AN: 152050 Hom.: 5495 Cov.: 32 AF XY: 0.265 AC XY: 19672 AN XY: 74308

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.224

Alfa AF: 0.251 Hom.: 889

Bravo AF: 0.260

Asia WGS AF: 0.318 AC: 1102 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.45
DANN	Benign	0.37

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: rs2066861; hg19: chr4-155527436;