15-33134566-G-A

Variant names:

• chr15-33134566-G-A
• rs2444962
• NM_001277313.2:c.1867+18482C>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.1867+18482C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0976 in 152,268 control chromosomes in the GnomAD database, including 1,674 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 0.098 (1674 hom., cov: 33)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FMN1	NM_001277313.2	c.1867+18482C>T		intron_variant	Intron 4 of 20	ENST00000616417.5	NP_001264242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FMN1	ENST00000616417.5	c.1867+18482C>T		intron_variant	Intron 4 of 20	5	NM_001277313.2	ENSP00000479134.1
FMN1	ENST00000561249.5	c.1867+18482C>T		intron_variant	Intron 1 of 15	5		ENSP00000453443.1
FMN1	ENST00000674090.1	n.170-42363C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0976 AC: 14850 AN: 152150 Hom.: 1669 Cov.: 33

Gnomad AFR AF: 0.0518

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.0641

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0625

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0976 AC: 14860 AN: 152268 Hom.: 1674 Cov.: 33 AF XY: 0.106 AC XY: 7870 AN XY: 74458

African (AFR) AF: 0.0516 AC: 2146 AN: 41564

American (AMR) AF: 0.190 AC: 2915 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0744 AC: 258 AN: 3470

East Asian (EAS) AF: 0.597 AC: 3087 AN: 5172

South Asian (SAS) AF: 0.253 AC: 1222 AN: 4822

European-Finnish (FIN) AF: 0.0641 AC: 680 AN: 10608

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0625 AC: 4252 AN: 68010

Other (OTH) AF: 0.105 AC: 221 AN: 2114

Alfa AF: 0.0847 Hom.: 2014

Bravo AF: 0.105

Asia WGS AF: 0.422 AC: 1462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.7
DANN	Benign	0.58
PhyloP100		1.5
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: rs2444962; hg19: chr15-33426767;