rs2956147

chr15-32967452-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001277313.2(FMN1):c.2987+1262C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,028 control chromosomes in the GnomAD database, including 22,137 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 0.52 (22137 hom., cov: 32)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FMN1	NM_001277313.2	c.2987+1262C>T		intron_variant		ENST00000616417.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FMN1	ENST00000616417.5	c.2987+1262C>T		intron_variant		5	NM_001277313.2	A2
FMN1	ENST00000334528.13	c.2318+1262C>T		intron_variant		1		P2
FMN1	ENST00000561249.5	c.2693+1262C>T		intron_variant		5		A2
FMN1	ENST00000672206.1	c.1253+1262C>T		intron_variant				A2

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79123 AN: 151910 Hom.: 22122 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.521 AC: 79160 AN: 152028 Hom.: 22137 Cov.: 32 AF XY: 0.525 AC XY: 38997 AN XY: 74324

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.539

Alfa AF: 0.571 Hom.: 6954

Bravo AF: 0.517

Asia WGS AF: 0.678 AC: 2353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	8.0
Dann	Benign	0.65

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

Publications

LitVar

Other links and lift over

dbSNP: rs2956147; hg19: chr15-33259653;