Variant rs717411 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001277313.2(FMN1):c.1867+30075C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0612 in 151,928 control chromosomes in the GnomAD database, including 299 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.061 ( 299 hom., cov: 31)

Consequence

FMN1
NM_001277313.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.287

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.082 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.1867+30075C>T		intron_variant		ENST00000616417.5	NP_001264242.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
FMN1	ENST00000616417.5 linkuse as main transcript	c.1867+30075C>T	intron_variant	5	NM_001277313.2	ENSP00000479134	A2	Q68DA7-1
FMN1	ENST00000561249.5 linkuse as main transcript	c.1867+30075C>T	intron_variant	5		ENSP00000453443	A2
FMN1	ENST00000674090.1 linkuse as main transcript	n.170-30770C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0611

AC:

9283

AN:

151810

Hom.:

297

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0509

Gnomad AMI

AF:

0.135

Gnomad AMR

AF:

0.0653

Gnomad ASJ

AF:

0.0637

Gnomad EAS

AF:

0.0717

Gnomad SAS

AF:

0.0888

Gnomad FIN

AF:

0.0765

Gnomad MID

AF:

0.0955

Gnomad NFE

AF:

0.0594

Gnomad OTH

AF:

0.0831

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0612

AC:

9296

AN:

151928

Hom.:

299

Cov.:

AF XY:

0.0624

AC XY:

4632

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.0509

Gnomad4 AMR

AF:

0.0651

Gnomad4 ASJ

AF:

0.0637

Gnomad4 EAS

AF:

0.0713

Gnomad4 SAS

AF:

0.0889

Gnomad4 FIN

AF:

0.0765

Gnomad4 NFE

AF:

0.0594

Gnomad4 OTH

AF:

0.0870

Alfa

AF:

0.0316

Hom.:

Bravo

AF:

0.0601

Asia WGS

AF:

0.0760

AC:

265

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.81

DANN

Benign

0.69

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over