Genetic Variant FMNL2:c.1314+88T>G (chr2-152617280-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_052905.4(FMNL2):c.1314+88T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 1,145,242 control chromosomes in the GnomAD database, including 62,920 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 0.36 ( 10186 hom., cov: 32)

Exomes 𝑓: 0.32 ( 52734 hom. )

Consequence

FMNL2
NM_052905.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0930

Publications

14 publications found

Variant links:

Genes affected

FMNL2 (HGNC:18267): (formin like 2) This gene encodes a formin-related protein. Formin-related proteins have been implicated in morphogenesis, cytokinesis, and cell polarity. Alternatively spliced transcript variants encoding different isoforms have been described but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]

FMNL2 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=-0.56).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052905.4. 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
	FMNL2	NM_052905.4	MANE Select	c.1314+88T>G		intron	N/A	NP_443137.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FMNL2	ENST00000288670.14	TSL:1 MANE Select	c.1314+88T>G	intron	N/A	ENSP00000288670.9	Q96PY5-3
FMNL2	ENST00000475377.3	TSL:5	c.1314+88T>G	intron	N/A	ENSP00000418959.3	C9IZY8
FMNL2	ENST00000850952.1		c.1314+88T>G	intron	N/A	ENSP00000521036.1	A0ABJ7H8L6

Frequencies

GnomAD3 genomes

AF:

0.357

AC:

54191

AN:

152006

Hom.:

10154

Cov.:

show subpopulations

Gnomad AFR

AF:

0.452

Gnomad AMI

AF:

0.338

Gnomad AMR

AF:

0.396

Gnomad ASJ

AF:

0.455

Gnomad EAS

AF:

0.285

Gnomad SAS

AF:

0.421

Gnomad FIN

AF:

0.208

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.307

Gnomad OTH

AF:

0.395

GnomAD4 exome

AF:

0.321

AC:

318831

AN:

993118

Hom.:

52734

AF XY:

0.325

AC XY:

164935

AN XY:

507744

show subpopulations

African (AFR)

AF:

0.466

AC:

10813

AN:

23204

American (AMR)

AF:

0.391

AC:

12502

AN:

31986

Ashkenazi Jewish (ASJ)

AF:

0.447

AC:

9116

AN:

20408

East Asian (EAS)

AF:

0.310

AC:

11472

AN:

36962

South Asian (SAS)

AF:

0.424

AC:

29303

AN:

69158

European-Finnish (FIN)

AF:

0.221

AC:

11341

AN:

51244

Middle Eastern (MID)

AF:

0.419

AC:

1988

AN:

4744

European-Non Finnish (NFE)

AF:

0.306

AC:

217308

AN:

710952

Other (OTH)

AF:

0.337

AC:

14988

AN:

44460

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

10509

21018

31528

42037

52546

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6092

12184

18276

24368

30460

<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:

0.357

AC:

54277

AN:

152124

Hom.:

10186

Cov.:

AF XY:

0.355

AC XY:

26416

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.452

AC:

18744

AN:

41474

American (AMR)

AF:

0.396

AC:

6060

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.455

AC:

1580

AN:

3472

East Asian (EAS)

AF:

0.285

AC:

1472

AN:

5162

South Asian (SAS)

AF:

0.423

AC:

2040

AN:

4824

European-Finnish (FIN)

AF:

0.208

AC:

2208

AN:

10596

Middle Eastern (MID)

AF:

0.432

AC:

127

AN:

294

European-Non Finnish (NFE)

AF:

0.307

AC:

20888

AN:

67986

Other (OTH)

AF:

0.403

AC:

850

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1814

3627

5441

7254

9068

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

524

1048

1572

2096

2620

<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:

0.328

Hom.:

14130

Bravo

AF:

0.372

Asia WGS

AF:

0.418

AC:

1453

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

(source)

DANN

Benign

0.63

PhyloP100

0.093

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