Variant 2-241413302-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_014808.4(FARP2):c.509-5C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00352 in 1,575,732 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0026 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0036 ( 5 hom. )

Consequence

FARP2
NM_014808.4 splice_region, intron

Scores

Splicing: ADA: 0.01455

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0380

Variant links:

Genes affected

FARP2 (HGNC:16460): (FERM, ARH/RhoGEF and pleckstrin domain protein 2) Enables guanyl-nucleotide exchange factor activity. Acts upstream of or within Rac protein signal transduction and neuron remodeling. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

FARP2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP6

Variant 2-241413302-C-G is Benign according to our data. Variant chr2-241413302-C-G is described in ClinVar as [Benign]. Clinvar id is 786496.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FARP2	NM_014808.4 linkuse as main transcript	c.509-5C>G		splice_region_variant, intron_variant		ENST00000264042.8	NP_055623.1	O94887-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FARP2	ENST00000264042.8 linkuse as main transcript	c.509-5C>G		splice_region_variant, intron_variant		1	NM_014808.4	ENSP00000264042.3		O94887-1

Frequencies

GnomAD3 genomes

AF:

0.00263

AC:

400

AN:

152172

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000628

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.00203

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.00207

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00431

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00250

AC:

572

AN:

228732

Hom.:

AF XY:

0.00261

AC XY:

319

AN XY:

122446

show subpopulations

Gnomad AFR exome

AF:

0.000142

Gnomad AMR exome

AF:

0.000874

Gnomad ASJ exome

AF:

0.000212

Gnomad EAS exome

AF:

0.000173

Gnomad SAS exome

AF:

0.00107

Gnomad FIN exome

AF:

0.00269

Gnomad NFE exome

AF:

0.00430

Gnomad OTH exome

AF:

0.00210

GnomAD4 exome

AF:

0.00362

AC:

5149

AN:

1423442

Hom.:

Cov.:

AF XY:

0.00354

AC XY:

2502

AN XY:

707484

show subpopulations

Gnomad4 AFR exome

AF:

0.000457

Gnomad4 AMR exome

AF:

0.000896

Gnomad4 ASJ exome

AF:

0.000510

Gnomad4 EAS exome

AF:

0.0000254

Gnomad4 SAS exome

AF:

0.000848

Gnomad4 FIN exome

AF:

0.00292

Gnomad4 NFE exome

AF:

0.00432

Gnomad4 OTH exome

AF:

0.00286

GnomAD4 genome

AF:

0.00263

AC:

400

AN:

152290

Hom.:

Cov.:

AF XY:

0.00255

AC XY:

190

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.000626

Gnomad4 AMR

AF:

0.00203

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.00207

Gnomad4 NFE

AF:

0.00431

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00375

Hom.:

Bravo

AF:

0.00240

Asia WGS

AF:

0.00144

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Aug 08, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.015

dbscSNV1_RF

Benign

0.15

SpliceAI score (max)

0.020

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over