Variant 15-32774277-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001277313.2(FMN1):c.*33G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 1,558,092 control chromosomes in the GnomAD database, including 13,507 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 1409 hom., cov: 32)

Exomes 𝑓: 0.13 ( 12098 hom. )

Consequence

FMN1
NM_001277313.2 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.712

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:

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 (BayesDel_noAF=-0.87).

BP6

Variant 15-32774277-C-T is Benign according to our data. Variant chr15-32774277-C-T is described in ClinVar as [Benign]. Clinvar id is 1238013.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 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.*33G>A		3_prime_UTR_variant	21/21	ENST00000616417.5	NP_001264242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FMN1	ENST00000616417.5 linkuse as main transcript	c.*33G>A		3_prime_UTR_variant	21/21	5	NM_001277313.2	ENSP00000479134	A2	Q68DA7-1

Frequencies

GnomAD3 genomes

AF:

0.133

AC:

20198

AN:

152062

Hom.:

1408

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.0548

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.153

Gnomad EAS

AF:

0.129

Gnomad SAS

AF:

0.131

Gnomad FIN

AF:

0.141

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.145

GnomAD3 exomes

AF:

0.127

AC:

27869

AN:

218698

Hom.:

1806

AF XY:

0.128

AC XY:

15029

AN XY:

117118

show subpopulations

Gnomad AFR exome

AF:

0.135

Gnomad AMR exome

AF:

0.119

Gnomad ASJ exome

AF:

0.151

Gnomad EAS exome

AF:

0.132

Gnomad SAS exome

AF:

0.121

Gnomad FIN exome

AF:

0.135

Gnomad NFE exome

AF:

0.126

Gnomad OTH exome

AF:

0.130

GnomAD4 exome

AF:

0.128

AC:

180633

AN:

1405912

Hom.:

12098

Cov.:

AF XY:

0.129

AC XY:

89840

AN XY:

699102

show subpopulations

Gnomad4 AFR exome

AF:

0.134

Gnomad4 AMR exome

AF:

0.123

Gnomad4 ASJ exome

AF:

0.152

Gnomad4 EAS exome

AF:

0.132

Gnomad4 SAS exome

AF:

0.125

Gnomad4 FIN exome

AF:

0.138

Gnomad4 NFE exome

AF:

0.127

Gnomad4 OTH exome

AF:

0.134

GnomAD4 genome

AF:

0.133

AC:

20222

AN:

152180

Hom.:

1409

Cov.:

AF XY:

0.132

AC XY:

9830

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.140

Gnomad4 AMR

AF:

0.125

Gnomad4 ASJ

AF:

0.153

Gnomad4 EAS

AF:

0.129

Gnomad4 SAS

AF:

0.132

Gnomad4 FIN

AF:

0.141

Gnomad4 NFE

AF:

0.129

Gnomad4 OTH

AF:

0.146

Alfa

AF:

0.135

Hom.:

1081

Bravo

AF:

0.135

Asia WGS

AF:

0.132

AC:

458

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

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 12, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.60

DANN

Benign

0.57

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