15-33125157-T-C

Position:

• chr15-33125157-T-C

Variant summary

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

The NM_001277313.2(FMN1):​c.1867+27891A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,206 control chromosomes in the GnomAD database, including 3,249 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 0.12 (3249 hom., cov: 33)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FMN1	NM_001277313.2	c.1867+27891A>G		intron_variant		ENST00000616417.5	NP_001264242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FMN1	ENST00000616417.5	c.1867+27891A>G		intron_variant		5	NM_001277313.2	ENSP00000479134	A2
FMN1	ENST00000561249.5	c.1867+27891A>G		intron_variant		5		ENSP00000453443	A2
FMN1	ENST00000674090.1	n.170-32954A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18144 AN: 152088 Hom.: 3235 Cov.: 33

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0399

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.0874

Gnomad SAS AF: 0.0534

Gnomad FIN AF: 0.00358

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.00453

Gnomad OTH AF: 0.0922

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

GnomAD4 genome AF: 0.120 AC: 18192 AN: 152206 Hom.: 3249 Cov.: 33 AF XY: 0.116 AC XY: 8606 AN XY: 74436

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.0397

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.0872

Gnomad4 SAS AF: 0.0526

Gnomad4 FIN AF: 0.00358

Gnomad4 NFE AF: 0.00454

Gnomad4 OTH AF: 0.0931

Alfa AF: 0.0358 Hom.: 257

Bravo AF: 0.134

Asia WGS AF: 0.0890 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.021
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7181962; hg19: chr15-33417358;