15-33098466-G-A

Variant names:

• chr15-33098466-G-A
• rs1026752
• NM_001277313.2:c.1868-9492C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001277313.2(FMN1):​c.1868-9492C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,046 control chromosomes in the GnomAD database, including 7,139 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 0.29 (7139 hom., cov: 32)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001277313.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FMN1	NM_001277313.2	MANE Select	c.1868-9492C>T		intron	N/A	NP_001264242.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FMN1	ENST00000616417.5	TSL:5 MANE Select	c.1868-9492C>T		intron	N/A	ENSP00000479134.1
	FMN1	ENST00000561249.5	TSL:5	c.1867+54582C>T		intron	N/A	ENSP00000453443.1
	FMN1	ENST00000672206.1		c.134-9492C>T		intron	N/A	ENSP00000500647.1

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43761 AN: 151928 Hom.: 7140 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.288 AC: 43765 AN: 152046 Hom.: 7139 Cov.: 32 AF XY: 0.291 AC XY: 21618 AN XY: 74308

African (AFR) AF: 0.135 AC: 5584 AN: 41490

American (AMR) AF: 0.371 AC: 5664 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1402 AN: 3468

East Asian (EAS) AF: 0.150 AC: 777 AN: 5168

South Asian (SAS) AF: 0.277 AC: 1335 AN: 4820

European-Finnish (FIN) AF: 0.398 AC: 4202 AN: 10562

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23715 AN: 67948

Other (OTH) AF: 0.299 AC: 630 AN: 2106

Alfa AF: 0.334 Hom.: 10383

Bravo AF: 0.282

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.50
PhyloP100		0.53
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1026752; hg19: chr15-33390667;