15-32776687-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001277313.2(FMN1):c.4215+147del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 444,468 control chromosomes in the GnomAD database, including 192 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.046 (184 hom., cov: 29)
  • Exomes 𝑓: 0.27 (8 hom.)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.533

Genes affected

FMN1 (HGNC:3768): (formin 1) This gene belongs to the formin homology family and encodes a protein that has a role in the formation of adherens junction and the polymerization of linear actin cables. The homologous gene in mouse is associated with limb deformity. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2015]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 15-32776687-CT-C is Benign according to our data. Variant chr15-32776687-CT-C is described in ClinVar as [Benign]. Clinvar id is 1256948.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FMN1	NM_001277313.2	c.4215+147del		intron_variant		ENST00000616417.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FMN1	ENST00000616417.5	c.4215+147del		intron_variant		5	NM_001277313.2	A2

Frequencies

GnomAD3 genomes AF: 0.0459 AC: 5611 AN: 122292 Hom.: 184 Cov.: 29

Gnomad AFR AF: 0.0489

Gnomad AMI AF: 0.00491

Gnomad AMR AF: 0.0887

Gnomad ASJ AF: 0.0158

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.0680

Gnomad FIN AF: 0.0737

Gnomad MID AF: 0.0325

Gnomad NFE AF: 0.0216

Gnomad OTH AF: 0.0396

GnomAD4 exome AF: 0.274 AC: 88269 AN: 322168 Hom.: 8 AF XY: 0.274 AC XY: 46429 AN XY: 169534

Gnomad4 AFR exome AF: 0.258

Gnomad4 AMR exome AF: 0.277

Gnomad4 ASJ exome AF: 0.273

Gnomad4 EAS exome AF: 0.292

Gnomad4 SAS exome AF: 0.244

Gnomad4 FIN exome AF: 0.282

Gnomad4 NFE exome AF: 0.276

Gnomad4 OTH exome AF: 0.279

GnomAD4 genome AF: 0.0459 AC: 5611 AN: 122300 Hom.: 184 Cov.: 29 AF XY: 0.0495 AC XY: 2913 AN XY: 58832

Gnomad4 AFR AF: 0.0488

Gnomad4 AMR AF: 0.0888

Gnomad4 ASJ AF: 0.0158

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.0685

Gnomad4 FIN AF: 0.0737

Gnomad4 NFE AF: 0.0216

Gnomad4 OTH AF: 0.0396

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

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs34593790; hg19: chr15-33068888;