15-32774521-CCCTA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001277313.2(FMN1):c.4216-171_4216-168del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0516 in 152,180 control chromosomes in the GnomAD database, including 296 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.052 (296 hom., cov: 32)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.771

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 -10 ACMG points.

• BP6: Variant 15-32774521-CCCTA-C is Benign according to our data. Variant chr15-32774521-CCCTA-C is described in ClinVar as [Benign]. Clinvar id is 1275341.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FMN1	NM_001277313.2	c.4216-171_4216-168del		intron_variant		ENST00000616417.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FMN1	ENST00000616417.5	c.4216-171_4216-168del		intron_variant		5	NM_001277313.2	A2

Frequencies

GnomAD3 genomes AF: 0.0517 AC: 7859 AN: 152062 Hom.: 298 Cov.: 32

Gnomad AFR AF: 0.0767

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0379

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0257

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0516 AC: 7853 AN: 152180 Hom.: 296 Cov.: 32 AF XY: 0.0529 AC XY: 3935 AN XY: 74402

Gnomad4 AFR AF: 0.0765

Gnomad4 AMR AF: 0.0378

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0257

Gnomad4 NFE AF: 0.0308

Gnomad4 OTH AF: 0.0487

Alfa AF: 0.0406 Hom.: 24

Bravo AF: 0.0529

Asia WGS AF: 0.161 AC: 556 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 12, 2021

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Computational scores

Source: dbNSFP v4.3

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: rs10540596; hg19: chr15-33066722;