chr15-32769558-A-G

Variant names:

• chr15-32769558-A-G
• rs1258725
• NM_001277313.2:c.*4752T>C

Variant summary

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

The NM_001277313.2(FMN1):​c.*4752T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,210 control chromosomes in the GnomAD database, including 39,873 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 0.71 (39873 hom., cov: 34)
  • Failed GnomAD Quality Control
• Consequence: FMN1 NM_001277313.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FMN1	NM_001277313.2	c.*4752T>C		3_prime_UTR_variant	Exon 21 of 21	ENST00000616417.5	NP_001264242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FMN1	ENST00000616417.5	c.*4752T>C		3_prime_UTR_variant	Exon 21 of 21	5	NM_001277313.2	ENSP00000479134.1
FMN1	ENST00000334528.13	c.*4752T>C		3_prime_UTR_variant	Exon 17 of 17	1		ENSP00000333950.9

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108202 AN: 152092 Hom.: 39836 Cov.: 34

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.735

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.711 AC: 108291 AN: 152210 Hom.: 39873 Cov.: 34 AF XY: 0.714 AC XY: 53124 AN XY: 74420

African (AFR) AF: 0.514 AC: 21319 AN: 41508

American (AMR) AF: 0.761 AC: 11634 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2573 AN: 3472

East Asian (EAS) AF: 0.638 AC: 3312 AN: 5194

South Asian (SAS) AF: 0.697 AC: 3367 AN: 4828

European-Finnish (FIN) AF: 0.869 AC: 9199 AN: 10590

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.799 AC: 54356 AN: 68018

Other (OTH) AF: 0.732 AC: 1546 AN: 2112

Alfa AF: 0.725 Hom.: 7996

Bravo AF: 0.694

Asia WGS AF: 0.649 AC: 2260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.50
PhyloP100		0.19
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: rs1258725; hg19: chr15-33061759;