Genetic Variant FARP2:c.1411+1893C>T (chr2-241443449-C-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_014808.4(FARP2):c.1411+1893C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,516 control chromosomes in the GnomAD database, including 1,192 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 0.11 ( 1191 hom., cov: 33)

Exomes 𝑓: 0.079 ( 1 hom. )

Consequence

FARP2
NM_014808.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.295

Publications

60 publications found

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:

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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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014808.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FARP2	NM_014808.4	MANE Select	c.1411+1893C>T	intron	N/A	NP_055623.1
FARP2	NM_001282983.2		c.1411+1893C>T	intron	N/A	NP_001269912.1
FARP2	NM_001282984.2		c.1411+1893C>T	intron	N/A	NP_001269913.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FARP2	ENST00000264042.8	TSL:1 MANE Select	c.1411+1893C>T	intron	N/A	ENSP00000264042.3
FARP2	ENST00000373287.8	TSL:1	c.1411+1893C>T	intron	N/A	ENSP00000362384.4
FARP2	ENST00000413432.2	TSL:2	c.*916C>T	3_prime_UTR	Exon 4 of 4	ENSP00000412772.2

Frequencies

GnomAD3 genomes

AF:

0.111

AC:

16820

AN:

152158

Hom.:

1192

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0302

Gnomad AMI

AF:

0.0484

Gnomad AMR

AF:

0.146

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.117

Gnomad SAS

AF:

0.103

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.150

Gnomad OTH

AF:

0.129

GnomAD4 exome

AF:

0.0792

AC:

AN:

240

Hom.:

Cov.:

AF XY:

0.0633

AC XY:

AN XY:

158

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.0938

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0706

AC:

AN:

170

Other (OTH)

AF:

0.188

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.534

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<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:

0.110

AC:

16813

AN:

152276

Hom.:

1191

Cov.:

AF XY:

0.108

AC XY:

8062

AN XY:

74456

show subpopulations

African (AFR)

AF:

0.0301

AC:

1251

AN:

41568

American (AMR)

AF:

0.146

AC:

2236

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.122

AC:

423

AN:

3468

East Asian (EAS)

AF:

0.117

AC:

605

AN:

5182

South Asian (SAS)

AF:

0.103

AC:

496

AN:

4832

European-Finnish (FIN)

AF:

0.118

AC:

1254

AN:

10608

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.150

AC:

10201

AN:

68006

Other (OTH)

AF:

0.129

AC:

273

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

762

1523

2285

3046

3808

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<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:

0.134

Hom.:

3472

Bravo

AF:

0.107

Asia WGS

AF:

0.100

AC:

348

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.1

(source)

DANN

Benign

0.69

PhyloP100

0.29

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