15-32769558-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.191
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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
FMN1NM_001277313.2 linkc.*4752T>C 3_prime_UTR_variant Exon 21 of 21 ENST00000616417.5 NP_001264242.1 Q68DA7-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FMN1ENST00000616417 linkc.*4752T>C 3_prime_UTR_variant Exon 21 of 21 5 NM_001277313.2 ENSP00000479134.1 Q68DA7-1
FMN1ENST00000334528 linkc.*4752T>C 3_prime_UTR_variant Exon 17 of 17 1 ENSP00000333950.9 Q68DA7-5

Frequencies

GnomAD3 genomes
AF:
0.711
AC:
108202
AN:
152092
Hom.:
39836
Cov.:
34
show subpopulations
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
GnomAD4 genome
AF:
0.711
AC:
108291
AN:
152210
Hom.:
39873
Cov.:
34
AF XY:
0.714
AC XY:
53124
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.514
Gnomad4 AMR
AF:
0.761
Gnomad4 ASJ
AF:
0.741
Gnomad4 EAS
AF:
0.638
Gnomad4 SAS
AF:
0.697
Gnomad4 FIN
AF:
0.869
Gnomad4 NFE
AF:
0.799
Gnomad4 OTH
AF:
0.732
Alfa
AF:
0.731
Hom.:
7894
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

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1258725; hg19: chr15-33061759; API