chr15-32920456-T-A

Position:

• chr15-32920456-T-A

Variant summary

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

The NM_001277313.2(FMN1):​c.3226+5718A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,024 control chromosomes in the GnomAD database, including 8,848 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 0.33 (8848 hom., cov: 32)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488

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 (NFE) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FMN1	NM_001277313.2	c.3226+5718A>T		intron_variant		ENST00000616417.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FMN1	ENST00000616417.5	c.3226+5718A>T		intron_variant		5	NM_001277313.2	A2

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50850 AN: 151906 Hom.: 8828 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.335 AC: 50900 AN: 152024 Hom.: 8848 Cov.: 32 AF XY: 0.331 AC XY: 24585 AN XY: 74328

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.316

Alfa AF: 0.366 Hom.: 1268

Bravo AF: 0.325

Asia WGS AF: 0.199 AC: 693 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	1.2
DANN	Benign	0.53

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: rs11635920; hg19: chr15-33212657;