dbSNP rs2282048: FARP1:c.171+31485A>G (chr13-98244898-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_001001715.4(FARP1):c.*189A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 1,412,636 control chromosomes in the GnomAD database, including 108,510 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 0.32 ( 9516 hom., cov: 32)

Exomes 𝑓: 0.39 ( 98994 hom. )

Consequence

FARP1
NM_001001715.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.63

Publications

13 publications found

Variant links:

Genes affected

FARP1 (HGNC:3591): (FERM, ARH/RhoGEF and pleckstrin domain protein 1) This gene encodes a protein containing a FERM (4.2, exrin, radixin, moesin) domain, a Dbl homology domain, and two pleckstrin homology domains. These domains are found in guanine nucleotide exchange factors and proteins that link the cytoskeleton to the cell membrane. The encoded protein functions in neurons to promote dendritic growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]

FARP1 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001715.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FARP1	NM_005766.4	MANE Select	c.171+31485A>G	intron	N/A	NP_005757.1
FARP1	NM_001001715.4		c.*189A>G	3_prime_UTR	Exon 3 of 3	NP_001001715.2
FARP1	NM_001286839.2		c.171+31485A>G	intron	N/A	NP_001273768.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FARP1	ENST00000319562.11	TSL:1 MANE Select	c.171+31485A>G	intron	N/A	ENSP00000322926.6
FARP1	ENST00000595437.5	TSL:1	c.171+31485A>G	intron	N/A	ENSP00000471242.1
FARP1	ENST00000376581.9	TSL:2	c.*189A>G	3_prime_UTR	Exon 3 of 3	ENSP00000365765.4

Frequencies

GnomAD3 genomes

AF:

0.323

AC:

49147

AN:

151970

Hom.:

9523

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.362

Gnomad AMR

AF:

0.381

Gnomad ASJ

AF:

0.462

Gnomad EAS

AF:

0.620

Gnomad SAS

AF:

0.409

Gnomad FIN

AF:

0.418

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.389

Gnomad OTH

AF:

0.378

GnomAD4 exome

AF:

0.390

AC:

491862

AN:

1260548

Hom.:

98994

Cov.:

AF XY:

0.392

AC XY:

239514

AN XY:

610456

show subpopulations

African (AFR)

AF:

0.0959

AC:

2662

AN:

27766

American (AMR)

AF:

0.369

AC:

7031

AN:

19032

Ashkenazi Jewish (ASJ)

AF:

0.465

AC:

8532

AN:

18334

East Asian (EAS)

AF:

0.650

AC:

21799

AN:

33526

South Asian (SAS)

AF:

0.409

AC:

24117

AN:

59012

European-Finnish (FIN)

AF:

0.427

AC:

11688

AN:

27390

Middle Eastern (MID)

AF:

0.502

AC:

1749

AN:

3486

European-Non Finnish (NFE)

AF:

0.386

AC:

393671

AN:

1019912

Other (OTH)

AF:

0.396

AC:

20613

AN:

52090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

14248

28495

42743

56990

71238

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13034

26068

39102

52136

65170

<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:

0.323

AC:

49153

AN:

152088

Hom.:

9516

Cov.:

AF XY:

0.329

AC XY:

24431

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.108

AC:

4467

AN:

41524

American (AMR)

AF:

0.380

AC:

5809

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.462

AC:

1602

AN:

3466

East Asian (EAS)

AF:

0.620

AC:

3202

AN:

5168

South Asian (SAS)

AF:

0.410

AC:

1972

AN:

4808

European-Finnish (FIN)

AF:

0.418

AC:

4414

AN:

10562

Middle Eastern (MID)

AF:

0.479

AC:

140

AN:

292

European-Non Finnish (NFE)

AF:

0.389

AC:

26416

AN:

67970

Other (OTH)

AF:

0.380

AC:

802

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1593

3186

4780

6373

7966

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

488

976

1464

1952

2440

<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:

0.371

Hom.:

16287

Bravo

AF:

0.312

Asia WGS

AF:

0.452

AC:

1576

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.18

(source)

DANN

Benign

0.21

PhyloP100

-1.6

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