Variant 2-152617280-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FMNL2	NM_052905.4 linkuse as main transcript	c.1314+88T>G		intron_variant		ENST00000288670.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FMNL2	ENST00000288670.14 linkuse as main transcript	c.1314+88T>G		intron_variant		1	NM_052905.4	P1	Q96PY5-3
FMNL2	ENST00000475377.3 linkuse as main transcript	c.1314+88T>G		intron_variant		5

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

Gnomad4 AFR exome

AF:

0.466

Gnomad4 AMR exome

AF:

0.391

Gnomad4 ASJ exome

AF:

0.447

Gnomad4 EAS exome

AF:

0.310

Gnomad4 SAS exome

AF:

0.424

Gnomad4 FIN exome

AF:

0.221

Gnomad4 NFE exome

AF:

0.306

Gnomad4 OTH exome

AF:

0.337

GnomAD4 genome

AF:

0.357

AC:

54277

AN:

152124

Hom.:

10186

Cov.:

AF XY:

0.355

AC XY:

26416

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.452

Gnomad4 AMR

AF:

0.396

Gnomad4 ASJ

AF:

0.455

Gnomad4 EAS

AF:

0.285

Gnomad4 SAS

AF:

0.423

Gnomad4 FIN

AF:

0.208

Gnomad4 NFE

AF:

0.307

Gnomad4 OTH

AF:

0.403

Alfa

AF:

0.321

Hom.:

10619

Bravo

AF:

0.372

Asia WGS

AF:

0.418

AC:

1453

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Benign

0.63

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over