rs12593365

Positions:

• chr15-32815789-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.3929-11457A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,100 control chromosomes in the GnomAD database, including 3,112 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 0.19 (3112 hom., cov: 32)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

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]

LOC107984089 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FMN1	NM_001277313.2	c.3929-11457A>G		intron_variant		ENST00000616417.5
LOC107984089	XR_002957769.2	n.277-1775T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FMN1	ENST00000616417.5	c.3929-11457A>G		intron_variant		5	NM_001277313.2	A2

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29606 AN: 151982 Hom.: 3106 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.195 AC: 29616 AN: 152100 Hom.: 3112 Cov.: 32 AF XY: 0.198 AC XY: 14718 AN XY: 74386

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.204

Alfa AF: 0.212 Hom.: 2374

Bravo AF: 0.189

Asia WGS AF: 0.282 AC: 979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.46
DANN	Benign	0.82

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

Other links and lift over

dbSNP: rs12593365; hg19: chr15-33107990;