rs7165427

chr15-32868059-C-T

Variant summary

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

The NM_001277313.2(FMN1):c.3836-10952G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,020 control chromosomes in the GnomAD database, including 35,214 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 0.67 (35214 hom., cov: 32)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FMN1	NM_001277313.2	c.3836-10952G>A		intron_variant		ENST00000616417.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FMN1	ENST00000616417.5	c.3836-10952G>A		intron_variant		5	NM_001277313.2	A2

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101665 AN: 151900 Hom.: 35170 Cov.: 32

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.669 AC: 101759 AN: 152020 Hom.: 35214 Cov.: 32 AF XY: 0.664 AC XY: 49332 AN XY: 74308

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.650

Alfa AF: 0.626 Hom.: 42644

Bravo AF: 0.674

Asia WGS AF: 0.610 AC: 2121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.0060
Dann	Benign	0.36

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: rs7165427; hg19: chr15-33160260;