Variant 15-32776688-T-TTC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001277313.2(FMN1):c.4215+146_4215+147insGA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 184,950 control chromosomes in the GnomAD database, including 1,493 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.15 ( 1340 hom., cov: 26)

Exomes 𝑓: 0.49 ( 153 hom. )

Consequence

FMN1
NM_001277313.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.641

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 15-32776688-T-TTC is Benign according to our data. Variant chr15-32776688-T-TTC is described in ClinVar as [Benign]. Clinvar id is 1275586.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 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.4215+146_4215+147insGA		intron_variant		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.4215+146_4215+147insGA		intron_variant		5	NM_001277313.2	ENSP00000479134	A2	Q68DA7-1

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

19626

AN:

127388

Hom.:

1340

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.0585

Gnomad AMR

AF:

0.156

Gnomad ASJ

AF:

0.164

Gnomad EAS

AF:

0.211

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.169

Gnomad MID

AF:

0.221

Gnomad NFE

AF:

0.143

Gnomad OTH

AF:

0.169

GnomAD4 exome

AF:

0.486

AC:

27970

AN:

57558

Hom.:

153

AF XY:

0.485

AC XY:

14455

AN XY:

29806

show subpopulations

Gnomad4 AFR exome

AF:

0.479

Gnomad4 AMR exome

AF:

0.484

Gnomad4 ASJ exome

AF:

0.494

Gnomad4 EAS exome

AF:

0.485

Gnomad4 SAS exome

AF:

0.483

Gnomad4 FIN exome

AF:

0.489

Gnomad4 NFE exome

AF:

0.486

Gnomad4 OTH exome

AF:

0.489

GnomAD4 genome

AF:

0.154

AC:

19640

AN:

127392

Hom.:

1340

Cov.:

AF XY:

0.155

AC XY:

9472

AN XY:

61292

show subpopulations

Gnomad4 AFR

AF:

0.164

Gnomad4 AMR

AF:

0.156

Gnomad4 ASJ

AF:

0.164

Gnomad4 EAS

AF:

0.210

Gnomad4 SAS

AF:

0.158

Gnomad4 FIN

AF:

0.169

Gnomad4 NFE

AF:

0.143

Gnomad4 OTH

AF:

0.170

Alfa

AF:

0.0179

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 13, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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