rs7165427

Variant names:

• chr15-32868059-C-T
• rs7165427
• NM_001277313.2:c.3836-10952G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FMN1	NM_001277313.2	c.3836-10952G>A		intron_variant	Intron 16 of 20	ENST00000616417.5	NP_001264242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FMN1	ENST00000616417.5	c.3836-10952G>A		intron_variant	Intron 16 of 20	5	NM_001277313.2	ENSP00000479134.1

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

African (AFR) AF: 0.847 AC: 35141 AN: 41502

American (AMR) AF: 0.554 AC: 8463 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2147 AN: 3468

East Asian (EAS) AF: 0.512 AC: 2639 AN: 5152

South Asian (SAS) AF: 0.640 AC: 3084 AN: 4818

European-Finnish (FIN) AF: 0.585 AC: 6160 AN: 10530

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 42021 AN: 67964

Other (OTH) AF: 0.650 AC: 1373 AN: 2112

Alfa AF: 0.631 Hom.: 60171

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
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7165427; hg19: chr15-33160260;