3-58085917-C-A

Position:

• chr3-58085917-C-A

Variant summary

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

The ENST00000295956.9(FLNB):​c.787+4141C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,004 control chromosomes in the GnomAD database, including 18,890 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 (18890 hom., cov: 31)
• Consequence: FLNB ENST00000295956.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

Genes affected

FLNB (HGNC:3755): (filamin B) This gene encodes a member of the filamin family. The encoded protein interacts with glycoprotein Ib alpha as part of the process to repair vascular injuries. The platelet glycoprotein Ib complex includes glycoprotein Ib alpha, and it binds the actin cytoskeleton. Mutations in this gene have been found in several conditions: atelosteogenesis type 1 and type 3; boomerang dysplasia; autosomal dominant Larsen syndrome; and spondylocarpotarsal synostosis syndrome. Multiple alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLNB	NM_001457.4	c.787+4141C>A		intron_variant		ENST00000295956.9	NP_001448.2
FLNB	NM_001164317.2	c.787+4141C>A		intron_variant			NP_001157789.1
FLNB	NM_001164318.2	c.787+4141C>A		intron_variant			NP_001157790.1
FLNB	NM_001164319.2	c.787+4141C>A		intron_variant			NP_001157791.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLNB	ENST00000295956.9	c.787+4141C>A		intron_variant		1	NM_001457.4	ENSP00000295956	A1

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70955 AN: 151886 Hom.: 18850 Cov.: 31

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.467 AC: 71052 AN: 152004 Hom.: 18890 Cov.: 31 AF XY: 0.476 AC XY: 35360 AN XY: 74304

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.447

Alfa AF: 0.359 Hom.: 17929

Bravo AF: 0.491

Asia WGS AF: 0.793 AC: 2756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.73

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

Publications

LitVar

Other links and lift over

dbSNP: rs4681784; hg19: chr3-58071644;