Genetic Variant FIGNL2:p.Gln448Arg (chr12-51821071-T-C) – ACMG Classification: Likely_benign (-1 pts)

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

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

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.37

Publications

0 publications found

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]

FIGNL2 links:

ENSG00000260473 (HGNC:):

ENSG00000260473 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.4109315).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001384995.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FIGNL2	NM_001384995.1	MANE Select	c.1343A>G	p.Gln448Arg	missense	Exon 2 of 2	NP_001371924.1	A6NMB9
FIGNL2	NM_001013690.5		c.1343A>G	p.Gln448Arg	missense	Exon 2 of 2	NP_001013712.4	A6NMB9
FIGNL2	NM_001384996.1		c.1343A>G	p.Gln448Arg	missense	Exon 3 of 3	NP_001371925.1	A6NMB9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
FIGNL2	ENST00000618634.3	TSL:5 MANE Select	c.1343A>G	p.Gln448Arg	missense	Exon 2 of 2	ENSP00000491257.1	A6NMB9
FIGNL2	ENST00000938505.1		c.1343A>G	p.Gln448Arg	missense	Exon 2 of 2	ENSP00000608564.1
FIGNL2	ENST00000948593.1		c.1343A>G	p.Gln448Arg	missense	Exon 2 of 2	ENSP00000618652.1

Frequencies

GnomAD3 genomes

AF:

0.000200

AC:

AN:

150218

Hom.:

Cov.:

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

GnomAD2 exomes

AF:

0.00

AC:

AN:

1652

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000143

AC:

162

AN:

1133216

Hom.:

Cov.:

AF XY:

0.000160

AC XY:

AN XY:

544178

show subpopulations

African (AFR)

AF:

0.00128

AC:

AN:

22652

American (AMR)

AF:

0.000847

AC:

AN:

8262

Ashkenazi Jewish (ASJ)

AF:

0.00108

AC:

AN:

14816

East Asian (EAS)

AF:

0.00

AC:

AN:

25624

South Asian (SAS)

AF:

0.0000838

AC:

AN:

35782

European-Finnish (FIN)

AF:

0.00

AC:

AN:

25412

Middle Eastern (MID)

AF:

0.00330

AC:

AN:

3030

European-Non Finnish (NFE)

AF:

0.0000798

AC:

AN:

952148

Other (OTH)

AF:

0.000462

AC:

AN:

45490

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000200

AC:

AN:

150326

Hom.:

Cov.:

AF XY:

0.000191

AC XY:

AN XY:

73472

show subpopulations

African (AFR)

AF:

0.0000969

AC:

AN:

41266

American (AMR)

AF:

0.000860

AC:

AN:

15118

Ashkenazi Jewish (ASJ)

AF:

0.000579

AC:

AN:

3456

East Asian (EAS)

AF:

0.00

AC:

AN:

5108

South Asian (SAS)

AF:

0.000207

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9814

Middle Eastern (MID)

AF:

0.0103

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0000890

AC:

AN:

67450

Other (OTH)

AF:

0.000480

AC:

AN:

2084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000142

Hom.:

Bravo

AF:

0.000283

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.23

BayesDel_noAF

Benign

-0.46

CADD

Benign

(source)

DANN

Benign

0.65

DEOGEN2

Uncertain

0.63

FATHMM_MKL

Uncertain

0.84

LIST_S2

Benign

0.57

MetaRNN

Benign

0.41

MutationAssessor

Benign

1.2

PhyloP100

5.4

PrimateAI

Pathogenic

0.93

Polyphen

0.013

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over