Variant 15-32798901-CCTT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PM4_SupportingBP6_Very_StrongBA1

The NM_001277313.2(FMN1):c.4030_4032del(p.Lys1344del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0389 in 1,613,356 control chromosomes in the GnomAD database, including 1,536 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.033 ( 125 hom., cov: 31)

Exomes 𝑓: 0.040 ( 1411 hom. )

Consequence

FMN1
NM_001277313.2 inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 7.64

Variant links:

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]

FMN1 links:

LOC107984089 (HGNC:):

LOC107984089 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_001277313.2. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 15-32798901-CCTT-C is Benign according to our data. Variant chr15-32798901-CCTT-C is described in ClinVar as [Benign]. Clinvar id is 194480.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-32798901-CCTT-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FMN1	NM_001277313.2 linkuse as main transcript	c.4030_4032del	p.Lys1344del	inframe_deletion	19/21	ENST00000616417.5	NP_001264242.1
LOC107984089	XR_002957769.2 linkuse as main transcript	n.198-12014_198-12012del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FMN1	ENST00000616417.5 linkuse as main transcript	c.4030_4032del	p.Lys1344del	inframe_deletion	19/21	5	NM_001277313.2	ENSP00000479134	A2	Q68DA7-1

Frequencies

GnomAD3 genomes

AF:

0.0329

AC:

5002

AN:

152126

Hom.:

123

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00864

Gnomad AMI

AF:

0.00330

Gnomad AMR

AF:

0.0801

Gnomad ASJ

AF:

0.0144

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0305

Gnomad FIN

AF:

0.0339

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0410

Gnomad OTH

AF:

0.0287

GnomAD3 exomes

AF:

0.0412

AC:

10239

AN:

248406

Hom.:

377

AF XY:

0.0384

AC XY:

5171

AN XY:

134778

show subpopulations

Gnomad AFR exome

AF:

0.00706

Gnomad AMR exome

AF:

0.119

Gnomad ASJ exome

AF:

0.0166

Gnomad EAS exome

AF:

0.0000557

Gnomad SAS exome

AF:

0.0267

Gnomad FIN exome

AF:

0.0336

Gnomad NFE exome

AF:

0.0367

Gnomad OTH exome

AF:

0.0370

GnomAD4 exome

AF:

0.0396

AC:

57799

AN:

1461112

Hom.:

1411

AF XY:

0.0390

AC XY:

28346

AN XY:

726848

show subpopulations

Gnomad4 AFR exome

AF:

0.00642

Gnomad4 AMR exome

AF:

0.113

Gnomad4 ASJ exome

AF:

0.0169

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.0283

Gnomad4 FIN exome

AF:

0.0329

Gnomad4 NFE exome

AF:

0.0411

Gnomad4 OTH exome

AF:

0.0365

GnomAD4 genome

AF:

0.0329

AC:

5007

AN:

152244

Hom.:

125

Cov.:

AF XY:

0.0336

AC XY:

2504

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.00862

Gnomad4 AMR

AF:

0.0805

Gnomad4 ASJ

AF:

0.0144

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.0307

Gnomad4 FIN

AF:

0.0339

Gnomad4 NFE

AF:

0.0410

Gnomad4 OTH

AF:

0.0279

Alfa

AF:

0.0116

Hom.:

Bravo

AF:

0.0339

Asia WGS

AF:

0.0180

AC:

AN:

3478

EpiCase

AF:

0.0360

EpiControl

AF:

0.0323

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 05, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

Oct 29, 2014

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over