chr15-33143978-G-A

Variant names:

• chr15-33143978-G-A
• rs2444975
• NM_001277313.2:c.1867+9070C>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+9070C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,994 control chromosomes in the GnomAD database, including 16,842 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 0.47 (16842 hom., cov: 32)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.976
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FMN1	NM_001277313.2	c.1867+9070C>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+9070C>T		intron_variant	Intron 4 of 20	5	NM_001277313.2	ENSP00000479134.1
FMN1	ENST00000561249.5	c.1867+9070C>T		intron_variant	Intron 1 of 15	5		ENSP00000453443.1
FMN1	ENST00000674090.1	n.169+36220C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70877 AN: 151874 Hom.: 16834 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.467 AC: 70919 AN: 151994 Hom.: 16842 Cov.: 32 AF XY: 0.462 AC XY: 34284 AN XY: 74282

African (AFR) AF: 0.443 AC: 18334 AN: 41400

American (AMR) AF: 0.477 AC: 7295 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1679 AN: 3470

East Asian (EAS) AF: 0.677 AC: 3502 AN: 5172

South Asian (SAS) AF: 0.462 AC: 2223 AN: 4810

European-Finnish (FIN) AF: 0.353 AC: 3727 AN: 10564

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.481 AC: 32685 AN: 67978

Other (OTH) AF: 0.467 AC: 985 AN: 2108

Alfa AF: 0.475 Hom.: 2190

Bravo AF: 0.475

Asia WGS AF: 0.578 AC: 2011 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.8
DANN	Benign	0.44
PhyloP100		0.98
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: rs2444975; hg19: chr15-33436179;