15-33073599-T-C

Position:

• chr15-33073599-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001277313.2(FMN1):​c.2044-8525A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,150 control chromosomes in the GnomAD database, including 52,477 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 0.83 (52477 hom., cov: 31)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

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]

LOC124903459 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FMN1	NM_001277313.2	c.2044-8525A>G		intron_variant		ENST00000616417.5	NP_001264242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FMN1	ENST00000616417.5	c.2044-8525A>G		intron_variant		5	NM_001277313.2	ENSP00000479134.1
FMN1	ENST00000561249.5	c.1868-65524A>G		intron_variant		5		ENSP00000453443.1
FMN1	ENST00000672206.1	c.310-8525A>G		intron_variant				ENSP00000500647.1
FMN1	ENST00000674090.1	n.417-8525A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126056 AN: 152032 Hom.: 52428 Cov.: 31

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.829 AC: 126166 AN: 152150 Hom.: 52477 Cov.: 31 AF XY: 0.832 AC XY: 61880 AN XY: 74366

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.854

Gnomad4 ASJ AF: 0.826

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.852

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.824

Alfa AF: 0.794 Hom.: 64504

Bravo AF: 0.834

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs345804; hg19: chr15-33365800;