dbSNP rs3771570: 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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FARP2	NM_014808.4 link	c.1411+1893C>T		intron_variant	Intron 13 of 26	ENST00000264042.8	NP_055623.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
FARP2	ENST00000264042.8 link	c.1411+1893C>T	intron_variant	Intron 13 of 26	1	NM_014808.4	ENSP00000264042.3
FARP2	ENST00000373287.8 link	c.1411+1893C>T	intron_variant	Intron 13 of 17	1		ENSP00000362384.4
FARP2	ENST00000413432.2 link	c.*916C>T	3_prime_UTR_variant	Exon 4 of 4	2		ENSP00000412772.2
FARP2	ENST00000627550.2 link	c.1411+1893C>T	intron_variant	Intron 13 of 17	2		ENSP00000486597.1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over