rs2956147

Variant names:

• chr15-32967452-G-A
• rs2956147
• NM_001277313.2:c.2987+1262C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001277313.2(FMN1):​c.2987+1262C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,028 control chromosomes in the GnomAD database, including 22,137 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 0.52 (22137 hom., cov: 32)
• Consequence: FMN1 NM_001277313.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FMN1	NM_001277313.2	c.2987+1262C>T		intron_variant	Intron 8 of 20	ENST00000616417.5	NP_001264242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FMN1	ENST00000616417.5	c.2987+1262C>T		intron_variant	Intron 8 of 20	5	NM_001277313.2	ENSP00000479134.1
FMN1	ENST00000334528.13	c.2318+1262C>T		intron_variant	Intron 4 of 16	1		ENSP00000333950.9
FMN1	ENST00000561249.5	c.2693+1262C>T		intron_variant	Intron 3 of 15	5		ENSP00000453443.1
FMN1	ENST00000672206.1	c.1253+1262C>T		intron_variant	Intron 5 of 17			ENSP00000500647.1

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79123 AN: 151910 Hom.: 22122 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.521 AC: 79160 AN: 152028 Hom.: 22137 Cov.: 32 AF XY: 0.525 AC XY: 38997 AN XY: 74324

African (AFR) AF: 0.297 AC: 12320 AN: 41438

American (AMR) AF: 0.648 AC: 9891 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2079 AN: 3472

East Asian (EAS) AF: 0.769 AC: 3967 AN: 5162

South Asian (SAS) AF: 0.620 AC: 2993 AN: 4828

European-Finnish (FIN) AF: 0.576 AC: 6091 AN: 10566

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39947 AN: 67972

Other (OTH) AF: 0.539 AC: 1138 AN: 2112

Alfa AF: 0.573 Hom.: 16363

Bravo AF: 0.517

Asia WGS AF: 0.678 AC: 2353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.0
DANN	Benign	0.65
PhyloP100		0.029
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: rs2956147; hg19: chr15-33259653;