NM_001384995.1:c.1343A>G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001384995.1(FIGNL2):​c.1343A>G​(p.Gln448Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00015 in 1,283,542 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00014 ( 0 hom. )

Consequence

FIGNL2
NM_001384995.1 missense

Scores

1
2
6

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.37
Variant links:
Genes affected
FIGNL2 (HGNC:13287): (fidgetin like 2) Predicted to enable microtubule-severing ATPase activity. Predicted to be involved in cytoplasmic microtubule organization. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.4109315).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FIGNL2NM_001384995.1 linkc.1343A>G p.Gln448Arg missense_variant Exon 2 of 2 ENST00000618634.3 NP_001371924.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FIGNL2ENST00000618634.3 linkc.1343A>G p.Gln448Arg missense_variant Exon 2 of 2 5 NM_001384995.1 ENSP00000491257.1 A6NMB9
ENSG00000260473ENST00000637934.1 linkn.177-2374T>C intron_variant Intron 2 of 4 5

Frequencies

GnomAD3 genomes
AF:
0.000200
AC:
30
AN:
150218
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000972
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000861
Gnomad ASJ
AF:
0.000579
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00955
Gnomad NFE
AF:
0.0000889
Gnomad OTH
AF:
0.000485
GnomAD4 exome
AF:
0.000143
AC:
162
AN:
1133216
Hom.:
0
Cov.:
29
AF XY:
0.000160
AC XY:
87
AN XY:
544178
show subpopulations
Gnomad4 AFR exome
AF:
0.00128
Gnomad4 AMR exome
AF:
0.000847
Gnomad4 ASJ exome
AF:
0.00108
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000838
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000798
Gnomad4 OTH exome
AF:
0.000462
GnomAD4 genome
AF:
0.000200
AC:
30
AN:
150326
Hom.:
0
Cov.:
32
AF XY:
0.000191
AC XY:
14
AN XY:
73472
show subpopulations
Gnomad4 AFR
AF:
0.0000969
Gnomad4 AMR
AF:
0.000860
Gnomad4 ASJ
AF:
0.000579
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000890
Gnomad4 OTH
AF:
0.000480
Alfa
AF:
0.000142
Hom.:
0
Bravo
AF:
0.000283

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Sep 27, 2021
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1343A>G (p.Q448R) alteration is located in exon 2 (coding exon 1) of the FIGNL2 gene. This alteration results from a A to G substitution at nucleotide position 1343, causing the glutamine (Q) at amino acid position 448 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.23
BayesDel_noAF
Benign
-0.46
CADD
Benign
22
DANN
Benign
0.65
DEOGEN2
Uncertain
0.63
D;D
FATHMM_MKL
Uncertain
0.84
D
LIST_S2
Benign
0.57
.;T
MetaRNN
Benign
0.41
T;T
MutationAssessor
Benign
1.2
L;L
PrimateAI
Pathogenic
0.93
D
Polyphen
0.013
B;B
GERP RS
2.8
Varity_R
0.066
gMVP
0.70

Splicing

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: rs868808853; hg19: chr12-52214855; API