dbSNP rs11858145: FMN1:p.Gly171Val (chr15-33067373-C-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001103184.4(FMN1):c.512G>T(p.Gly171Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 1,613,658 control chromosomes in the GnomAD database, including 352,234 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.65 ( 32801 hom., cov: 31)

Exomes 𝑓: 0.66 ( 319433 hom. )

Consequence

FMN1
NM_001103184.4 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.736

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:

LOC124903459 (HGNC:):

LOC124903459 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=9.604586E-7).

BP6

Variant 15-33067373-C-A is Benign according to our data. Variant chr15-33067373-C-A is described in ClinVar as [Benign]. Clinvar id is 1231319.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FMN1	NM_001277313.2 link	c.2044-2299G>T		intron_variant	Intron 5 of 20	ENST00000616417.5	NP_001264242.1	Q68DA7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FMN1	ENST00000616417.5 link	c.2044-2299G>T		intron_variant	Intron 5 of 20	5	NM_001277313.2	ENSP00000479134.1		Q68DA7-1

Frequencies

GnomAD3 genomes

AF:

0.653

AC:

99167

AN:

151864

Hom.:

32774

Cov.:

show subpopulations

Gnomad AFR

AF:

0.600

Gnomad AMI

AF:

0.721

Gnomad AMR

AF:

0.749

Gnomad ASJ

AF:

0.738

Gnomad EAS

AF:

0.840

Gnomad SAS

AF:

0.799

Gnomad FIN

AF:

0.662

Gnomad MID

AF:

0.623

Gnomad NFE

AF:

0.632

Gnomad OTH

AF:

0.675

GnomAD3 exomes

AF:

0.701

AC:

174559

AN:

249028

Hom.:

62257

AF XY:

0.701

AC XY:

94746

AN XY:

135074

show subpopulations

Gnomad AFR exome

AF:

0.597

Gnomad AMR exome

AF:

0.818

Gnomad ASJ exome

AF:

0.738

Gnomad EAS exome

AF:

0.834

Gnomad SAS exome

AF:

0.797

Gnomad FIN exome

AF:

0.659

Gnomad NFE exome

AF:

0.638

Gnomad OTH exome

AF:

0.687

GnomAD4 exome

AF:

0.658

AC:

961820

AN:

1461676

Hom.:

319433

Cov.:

AF XY:

0.661

AC XY:

480754

AN XY:

727122

show subpopulations

Gnomad4 AFR exome

AF:

0.601

Gnomad4 AMR exome

AF:

0.807

Gnomad4 ASJ exome

AF:

0.736

Gnomad4 EAS exome

AF:

0.852

Gnomad4 SAS exome

AF:

0.793

Gnomad4 FIN exome

AF:

0.654

Gnomad4 NFE exome

AF:

0.633

Gnomad4 OTH exome

AF:

0.679

GnomAD4 genome

AF:

0.653

AC:

99246

AN:

151982

Hom.:

32801

Cov.:

AF XY:

0.661

AC XY:

49067

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.600

Gnomad4 AMR

AF:

0.750

Gnomad4 ASJ

AF:

0.738

Gnomad4 EAS

AF:

0.841

Gnomad4 SAS

AF:

0.798

Gnomad4 FIN

AF:

0.662

Gnomad4 NFE

AF:

0.632

Gnomad4 OTH

AF:

0.677

Alfa

AF:

0.649

Hom.:

79566

Bravo

AF:

0.657

TwinsUK

AF:

0.640

AC:

2372

ALSPAC

AF:

0.617

AC:

2377

ESP6500AA

AF:

0.600

AC:

2309

ESP6500EA

AF:

0.648

AC:

5361

ExAC

AF:

0.695

AC:

83986

Asia WGS

AF:

0.812

AC:

2820

AN:

3478

EpiCase

AF:

0.634

EpiControl

AF:

0.644

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

May 04, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.79

BayesDel_noAF

Benign

-0.77

CADD

Benign

1.1

DANN

Benign

0.64

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.017

MetaRNN

Benign

9.6e-7

T;T

MetaSVM

Benign

-0.96

PROVEAN

Benign

1.4

N;N

REVEL

Benign

0.020

Sift

Benign

1.0

T;T

Sift4G

Benign

0.72

T;T

Polyphen

0.0

B;B

Vest4

0.093

MPC

0.024

ClinPred

0.0012

GERP RS

1.0

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