15-32776688-T-TTC

Variant summary

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

The NM_001277313.2(FMN1):c.4215+146_4215+147insGA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 184,950 control chromosomes in the GnomAD database, including 1,493 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.15 (1340 hom., cov: 26)
  • Exomes 𝑓: 0.49 (153 hom.)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.641

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 15-32776688-T-TTC is Benign according to our data. Variant chr15-32776688-T-TTC is described in ClinVar as [Benign]. Clinvar id is 1275586.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FMN1	NM_001277313.2	c.4215+146_4215+147insGA		intron_variant		ENST00000616417.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FMN1	ENST00000616417.5	c.4215+146_4215+147insGA		intron_variant		5	NM_001277313.2	A2

Frequencies

GnomAD3 genomes AF: 0.154 AC: 19626 AN: 127388 Hom.: 1340 Cov.: 26

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.0585

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.221

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.169

GnomAD4 exome AF: 0.486 AC: 27970 AN: 57558 Hom.: 153 AF XY: 0.485 AC XY: 14455 AN XY: 29806

Gnomad4 AFR exome AF: 0.479

Gnomad4 AMR exome AF: 0.484

Gnomad4 ASJ exome AF: 0.494

Gnomad4 EAS exome AF: 0.485

Gnomad4 SAS exome AF: 0.483

Gnomad4 FIN exome AF: 0.489

Gnomad4 NFE exome AF: 0.486

Gnomad4 OTH exome AF: 0.489

GnomAD4 genome AF: 0.154 AC: 19640 AN: 127392 Hom.: 1340 Cov.: 26 AF XY: 0.155 AC XY: 9472 AN XY: 61292

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.170

Alfa AF: 0.0179 Hom.: 0

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 13, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs71818992; hg19: chr15-33068889;