15-33122973-G-A

Variant names:

• chr15-33122973-G-A
• rs717411
• NM_001277313.2:c.1867+30075C>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+30075C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0612 in 151,928 control chromosomes in the GnomAD database, including 299 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 0.061 (299 hom., cov: 31)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.082 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FMN1	NM_001277313.2	c.1867+30075C>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+30075C>T		intron_variant	Intron 4 of 20	5	NM_001277313.2	ENSP00000479134.1
FMN1	ENST00000561249.5	c.1867+30075C>T		intron_variant	Intron 1 of 15	5		ENSP00000453443.1
FMN1	ENST00000674090.1	n.170-30770C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0611 AC: 9283 AN: 151810 Hom.: 297 Cov.: 31

Gnomad AFR AF: 0.0509

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0653

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.0717

Gnomad SAS AF: 0.0888

Gnomad FIN AF: 0.0765

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0594

Gnomad OTH AF: 0.0831

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

GnomAD4 genome AF: 0.0612 AC: 9296 AN: 151928 Hom.: 299 Cov.: 31 AF XY: 0.0624 AC XY: 4632 AN XY: 74234

African (AFR) AF: 0.0509 AC: 2108 AN: 41424

American (AMR) AF: 0.0651 AC: 992 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3468

East Asian (EAS) AF: 0.0713 AC: 369 AN: 5178

South Asian (SAS) AF: 0.0889 AC: 427 AN: 4802

European-Finnish (FIN) AF: 0.0765 AC: 805 AN: 10522

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.0594 AC: 4037 AN: 67998

Other (OTH) AF: 0.0870 AC: 183 AN: 2104

Alfa AF: 0.0320 Hom.: 22

Bravo AF: 0.0601

Asia WGS AF: 0.0760 AC: 265 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.81
DANN	Benign	0.69
PhyloP100		-0.29
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: rs717411; hg19: chr15-33415174;