15-33119812-T-G

Variant names:

• chr15-33119812-T-G
• rs2444955
• NM_001277313.2:c.1868-30838A>C

Variant summary

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

The NM_001277313.2(FMN1):​c.1868-30838A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 152,050 control chromosomes in the GnomAD database, including 33,199 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 0.64 (33199 hom., cov: 32)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.669
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 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.1868-30838A>C		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.1868-30838A>C		intron	N/A	ENSP00000479134.1
	FMN1	ENST00000561249.5	TSL:5	c.1867+33236A>C		intron	N/A	ENSP00000453443.1
	FMN1	ENST00000674090.1		n.170-27609A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97492 AN: 151932 Hom.: 33189 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.641 AC: 97535 AN: 152050 Hom.: 33199 Cov.: 32 AF XY: 0.648 AC XY: 48171 AN XY: 74336

African (AFR) AF: 0.390 AC: 16172 AN: 41462

American (AMR) AF: 0.774 AC: 11828 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2636 AN: 3470

East Asian (EAS) AF: 0.798 AC: 4125 AN: 5170

South Asian (SAS) AF: 0.757 AC: 3646 AN: 4814

European-Finnish (FIN) AF: 0.718 AC: 7603 AN: 10582

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.725 AC: 49293 AN: 67966

Other (OTH) AF: 0.669 AC: 1411 AN: 2110

Alfa AF: 0.696 Hom.: 85215

Bravo AF: 0.633

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.9
DANN	Benign	0.53
PhyloP100		0.67
PromoterAI		0.012	Neutral
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: rs2444955; hg19: chr15-33412013;