Genetic Variant FIGN:c.26-870C>A (chr2-163612676-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018086.4(FIGN):c.26-870C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 914,732 control chromosomes in the GnomAD database, including 170,097 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 0.46 ( 18554 hom., cov: 26)

Exomes 𝑓: 0.62 ( 151543 hom. )

Consequence

FIGN
NM_018086.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.11

Publications

8 publications found

Variant links:

Genes affected

FIGN (HGNC:13285): (fidgetin, microtubule severing factor) Predicted to enable microtubule-severing ATPase activity. Predicted to be involved in cytoplasmic microtubule organization. Predicted to act upstream of or within locomotory behavior. Predicted to be located in nuclear matrix. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

FIGN links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018086.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FIGN	NM_018086.4	MANE Select	c.26-870C>A		intron	N/A	NP_060556.2	Q5HY92
	FIGN	NM_001321825.2		c.-8-870C>A		intron	N/A	NP_001308754.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FIGN	ENST00000333129.4	TSL:1 MANE Select	c.26-870C>A	intron	N/A	ENSP00000333836.3	Q5HY92
FIGN	ENST00000879555.1		c.26-870C>A	intron	N/A	ENSP00000549614.1
FIGN	ENST00000409634.5	TSL:5	c.26-18880C>A	intron	N/A	ENSP00000386768.1	B8ZZS6

Frequencies

GnomAD3 genomes

AF:

0.464

AC:

66985

AN:

144410

Hom.:

18565

Cov.:

show subpopulations

Gnomad AFR

AF:

0.131

Gnomad AMI

AF:

0.775

Gnomad AMR

AF:

0.437

Gnomad ASJ

AF:

0.501

Gnomad EAS

AF:

0.443

Gnomad SAS

AF:

0.528

Gnomad FIN

AF:

0.583

Gnomad MID

AF:

0.507

Gnomad NFE

AF:

0.627

Gnomad OTH

AF:

0.475

GnomAD4 exome

AF:

0.623

AC:

479967

AN:

770220

Hom.:

151543

AF XY:

0.625

AC XY:

223712

AN XY:

357798

show subpopulations

African (AFR)

AF:

0.0874

AC:

1251

AN:

14306

American (AMR)

AF:

0.411

AC:

367

AN:

892

Ashkenazi Jewish (ASJ)

AF:

0.517

AC:

2447

AN:

4736

East Asian (EAS)

AF:

0.424

AC:

1399

AN:

3302

South Asian (SAS)

AF:

0.546

AC:

8255

AN:

15108

European-Finnish (FIN)

AF:

0.620

AC:

160

AN:

258

Middle Eastern (MID)

AF:

0.473

AC:

711

AN:

1502

European-Non Finnish (NFE)

AF:

0.640

AC:

451172

AN:

705066

Other (OTH)

AF:

0.567

AC:

14205

AN:

25050

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.516

Heterozygous variant carriers

8151

16302

24453

32604

40755

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16206

32412

48618

64824

81030

<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:

0.463

AC:

66957

AN:

144512

Hom.:

18554

Cov.:

AF XY:

0.462

AC XY:

32410

AN XY:

70148

show subpopulations

African (AFR)

AF:

0.131

AC:

4890

AN:

37346

American (AMR)

AF:

0.437

AC:

6248

AN:

14300

Ashkenazi Jewish (ASJ)

AF:

0.501

AC:

1719

AN:

3432

East Asian (EAS)

AF:

0.444

AC:

2199

AN:

4950

South Asian (SAS)

AF:

0.527

AC:

2382

AN:

4522

European-Finnish (FIN)

AF:

0.583

AC:

5602

AN:

9610

Middle Eastern (MID)

AF:

0.500

AC:

142

AN:

284

European-Non Finnish (NFE)

AF:

0.627

AC:

42143

AN:

67172

Other (OTH)

AF:

0.469

AC:

939

AN:

2002

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1473

2946

4420

5893

7366

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

606

1212

1818

2424

3030

<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:

0.549

Hom.:

71633

Bravo

AF:

0.418

Asia WGS

AF:

0.417

AC:

1449

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.8

(source)

DANN

Benign

0.67

PhyloP100

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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