Genetic Variant NM_014808.4:c.331+77A>G (chr2-241404918-A-G) – 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.331+77A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,091,714 control chromosomes in the GnomAD database, including 6,080 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 0.10 ( 846 hom., cov: 33)

Exomes 𝑓: 0.10 ( 5234 hom. )

Consequence

FARP2
NM_014808.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.296

Publications

29 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=-0.94).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FARP2	NM_014808.4 link	c.331+77A>G		intron_variant	Intron 4 of 26	ENST00000264042.8	NP_055623.1	O94887-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FARP2	ENST00000264042.8 link	c.331+77A>G		intron_variant	Intron 4 of 26	1	NM_014808.4	ENSP00000264042.3		O94887-1

Frequencies

GnomAD3 genomes

AF:

0.100

AC:

15285

AN:

152106

Hom.:

844

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.0713

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.157

Gnomad EAS

AF:

0.0298

Gnomad SAS

AF:

0.0753

Gnomad FIN

AF:

0.0683

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.0969

GnomAD4 exome

AF:

0.104

AC:

97436

AN:

939490

Hom.:

5234

AF XY:

0.103

AC XY:

50354

AN XY:

487858

show subpopulations

African (AFR)

AF:

0.108

AC:

2554

AN:

23566

American (AMR)

AF:

0.0996

AC:

4251

AN:

42678

Ashkenazi Jewish (ASJ)

AF:

0.151

AC:

3370

AN:

22256

East Asian (EAS)

AF:

0.0506

AC:

1880

AN:

37174

South Asian (SAS)

AF:

0.0789

AC:

5804

AN:

73576

European-Finnish (FIN)

AF:

0.0767

AC:

3908

AN:

50928

Middle Eastern (MID)

AF:

0.124

AC:

584

AN:

4698

European-Non Finnish (NFE)

AF:

0.110

AC:

70753

AN:

641616

Other (OTH)

AF:

0.101

AC:

4332

AN:

42998

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

4151

8301

12452

16602

20753

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1968

3936

5904

7872

9840

<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:

0.101

AC:

15299

AN:

152224

Hom.:

846

Cov.:

AF XY:

0.0975

AC XY:

7260

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.102

AC:

4256

AN:

41532

American (AMR)

AF:

0.104

AC:

1589

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.157

AC:

546

AN:

3470

East Asian (EAS)

AF:

0.0301

AC:

156

AN:

5188

South Asian (SAS)

AF:

0.0756

AC:

364

AN:

4816

European-Finnish (FIN)

AF:

0.0683

AC:

724

AN:

10604

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.108

AC:

7361

AN:

67994

Other (OTH)

AF:

0.0959

AC:

203

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

711

1422

2133

2844

3555

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

166

332

498

664

830

<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:

0.105

Hom.:

1491

Bravo

AF:

0.101

Asia WGS

AF:

0.0540

AC:

188

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.91

(source)

DANN

Benign

0.26

PhyloP100

-0.30

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