15-33046889-C-T

Variant names:

• chr15-33046889-C-T
• rs343906
• NM_001277313.2:c.2161+18068G>A

Variant summary

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

The NM_001277313.2(FMN1):​c.2161+18068G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,090 control chromosomes in the GnomAD database, including 41,339 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 0.73 (41339 hom., cov: 32)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FMN1	NM_001277313.2	MANE Select	c.2161+18068G>A		intron	N/A	NP_001264242.1	Q68DA7-1
	FMN1	NM_001103184.4		c.1492+18068G>A		intron	N/A	NP_001096654.1	Q68DA7-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FMN1	ENST00000616417.5	TSL:5 MANE Select	c.2161+18068G>A		intron	N/A	ENSP00000479134.1	Q68DA7-1
	FMN1	ENST00000334528.13	TSL:1	c.1492+18068G>A		intron	N/A	ENSP00000333950.9	Q68DA7-5
	FMN1	ENST00000561249.5	TSL:5	c.1868-38814G>A		intron	N/A	ENSP00000453443.1	H0YM30

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111521 AN: 151972 Hom.: 41312 Cov.: 32

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.734 AC: 111593 AN: 152090 Hom.: 41339 Cov.: 32 AF XY: 0.730 AC XY: 54288 AN XY: 74330

African (AFR) AF: 0.751 AC: 31165 AN: 41476

American (AMR) AF: 0.727 AC: 11101 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2642 AN: 3472

East Asian (EAS) AF: 0.410 AC: 2114 AN: 5160

South Asian (SAS) AF: 0.609 AC: 2938 AN: 4828

European-Finnish (FIN) AF: 0.780 AC: 8236 AN: 10560

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51076 AN: 67998

Other (OTH) AF: 0.704 AC: 1487 AN: 2112

Alfa AF: 0.754 Hom.: 6788

Bravo AF: 0.733

Asia WGS AF: 0.511 AC: 1782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.86
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs343906; hg19: chr15-33339090;