rs1534596

Variant names:

• chr15-32822681-A-C
• rs1534596
• NM_001277313.2:c.3929-18349T>G

Your query was ambiguous. Multiple possible variants found:

• chr15-32822681-A-C
• chr15-32822681-A-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.3929-18349T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,948 control chromosomes in the GnomAD database, including 11,460 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 0.37 (11460 hom., cov: 32)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FMN1	NM_001277313.2	MANE Select	c.3929-18349T>G		intron	N/A	NP_001264242.1	Q68DA7-1
	FMN1	NM_001103184.4		c.3260-18349T>G		intron	N/A	NP_001096654.1	Q68DA7-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FMN1	ENST00000616417.5	TSL:5 MANE Select	c.3929-18349T>G		intron	N/A	ENSP00000479134.1	Q68DA7-1
	FMN1	ENST00000334528.13	TSL:1	c.3260-18349T>G		intron	N/A	ENSP00000333950.9	Q68DA7-5
	FMN1	ENST00000561249.5	TSL:5	c.3635-18349T>G		intron	N/A	ENSP00000453443.1	H0YM30

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56735 AN: 151830 Hom.: 11457 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.374 AC: 56773 AN: 151948 Hom.: 11460 Cov.: 32 AF XY: 0.378 AC XY: 28037 AN XY: 74268

African (AFR) AF: 0.310 AC: 12853 AN: 41414

American (AMR) AF: 0.361 AC: 5508 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1356 AN: 3470

East Asian (EAS) AF: 0.860 AC: 4442 AN: 5168

South Asian (SAS) AF: 0.479 AC: 2300 AN: 4804

European-Finnish (FIN) AF: 0.375 AC: 3957 AN: 10548

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25222 AN: 67962

Other (OTH) AF: 0.385 AC: 811 AN: 2106

Alfa AF: 0.372 Hom.: 9320

Bravo AF: 0.371

Asia WGS AF: 0.650 AC: 2257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.88
PhyloP100		-2.1
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: rs1534596; hg19: chr15-33114882;