15-32966780-A-C

Variant names:

• chr15-32966780-A-C
• rs2928023
• NM_001277313.2:c.2987+1934T>G

Variant summary

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

The NM_001277313.2(FMN1):​c.2987+1934T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,216 control chromosomes in the GnomAD database, including 49,867 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 0.81 (49867 hom., cov: 33)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FMN1	NM_001277313.2	c.2987+1934T>G		intron_variant	Intron 8 of 20	ENST00000616417.5	NP_001264242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FMN1	ENST00000616417.5	c.2987+1934T>G		intron_variant	Intron 8 of 20	5	NM_001277313.2	ENSP00000479134.1
FMN1	ENST00000334528.13	c.2318+1934T>G		intron_variant	Intron 4 of 16	1		ENSP00000333950.9
FMN1	ENST00000561249.5	c.2693+1934T>G		intron_variant	Intron 3 of 15	5		ENSP00000453443.1
FMN1	ENST00000672206.1	c.1253+1934T>G		intron_variant	Intron 5 of 17			ENSP00000500647.1

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122899 AN: 152098 Hom.: 49818 Cov.: 33

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.808 AC: 123004 AN: 152216 Hom.: 49867 Cov.: 33 AF XY: 0.808 AC XY: 60141 AN XY: 74422

African (AFR) AF: 0.772 AC: 32072 AN: 41536

American (AMR) AF: 0.867 AC: 13263 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3014 AN: 3470

East Asian (EAS) AF: 0.969 AC: 5020 AN: 5182

South Asian (SAS) AF: 0.849 AC: 4090 AN: 4820

European-Finnish (FIN) AF: 0.769 AC: 8137 AN: 10582

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54600 AN: 68000

Other (OTH) AF: 0.829 AC: 1755 AN: 2116

Alfa AF: 0.810 Hom.: 35890

Bravo AF: 0.816

Asia WGS AF: 0.903 AC: 3139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.63
PhyloP100		-0.86
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: rs2928023; hg19: chr15-33258981;