2-241413302-C-G

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

2
Splicing: ADA: 0.01455
2

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]

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
FARP2NM_014808.4 linkuse as main transcriptc.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
FARP2ENST00000264042.8 linkuse as main transcriptc.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.:
0
Cov.:
32
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.:
0
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.:
5
Cov.:
27
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.:
0
Cov.:
32
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.:
0
Bravo
AF:
0.00240
Asia WGS
AF:
0.00144
AC:
5
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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 08, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
CADD
Benign
11
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.

Other links and lift over

dbSNP: rs145651106; hg19: chr2-242352717; API