15-32996723-C-T

Variant names:

• chr15-32996723-C-T
• rs1871362
• NM_001277313.2:c.2223+11291G>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.2223+11291G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 152,024 control chromosomes in the GnomAD database, including 23,238 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 0.54 (23238 hom., cov: 33)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FMN1	NM_001277313.2	c.2223+11291G>A		intron_variant	Intron 7 of 20	ENST00000616417.5	NP_001264242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FMN1	ENST00000616417.5	c.2223+11291G>A		intron_variant	Intron 7 of 20	5	NM_001277313.2	ENSP00000479134.1
FMN1	ENST00000334528.13	c.1554+11291G>A		intron_variant	Intron 3 of 16	1		ENSP00000333950.9
FMN1	ENST00000561249.5	c.1929+11291G>A		intron_variant	Intron 2 of 15	5		ENSP00000453443.1
FMN1	ENST00000672206.1	c.489+11291G>A		intron_variant	Intron 4 of 17			ENSP00000500647.1

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82036 AN: 151904 Hom.: 23182 Cov.: 33

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.540 AC: 82150 AN: 152024 Hom.: 23238 Cov.: 33 AF XY: 0.533 AC XY: 39623 AN XY: 74298

African (AFR) AF: 0.707 AC: 29344 AN: 41484

American (AMR) AF: 0.473 AC: 7228 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2091 AN: 3468

East Asian (EAS) AF: 0.385 AC: 1987 AN: 5166

South Asian (SAS) AF: 0.446 AC: 2151 AN: 4822

European-Finnish (FIN) AF: 0.416 AC: 4385 AN: 10536

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33134 AN: 67966

Other (OTH) AF: 0.565 AC: 1192 AN: 2108

Alfa AF: 0.507 Hom.: 69671

Bravo AF: 0.551

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.28
DANN	Benign	0.55
PhyloP100		-1.2
Mutation Taster		=95/5	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: rs1871362; hg19: chr15-33288924;