Variant 13-98448293-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_005766.4(FARP1):c.3114T>C(p.Ser1038Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 1,612,630 control chromosomes in the GnomAD database, including 259,699 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 0.54 ( 22512 hom., cov: 33)

Exomes 𝑓: 0.57 ( 237187 hom. )

Consequence

FARP1
NM_005766.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.127

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:

STK24 (HGNC:11403): (serine/threonine kinase 24) This gene encodes a serine/threonine protein kinase that functions upstream of mitogen-activated protein kinase (MAPK) signaling. The encoded protein is cleaved into two chains by caspases; the N-terminal fragment (MST3/N) translocates to the nucleus and promotes programmed cells death. There is a pseudogene for this gene on chromosome X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]

STK24 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP7

Synonymous conserved (PhyloP=0.127 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FARP1	NM_005766.4 linkuse as main transcript	c.3114T>C	p.Ser1038Ser	synonymous_variant	27/27	ENST00000319562.11	NP_005757.1	Q9Y4F1-1A0A2X0TVY0
STK24	NM_001032296.4 linkuse as main transcript	c.*4880A>G		3_prime_UTR_variant	11/11	ENST00000539966.6	NP_001027467.2	Q9Y6E0-2Q5U0E6Q6P0Y1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
FARP1	ENST00000319562.11 linkuse as main transcript	c.3114T>C	p.Ser1038Ser	synonymous_variant	27/27	1	NM_005766.4	ENSP00000322926.6	Q9Y4F1-1
FARP1	ENST00000595437.5 linkuse as main transcript	c.3207T>C	p.Ser1069Ser	synonymous_variant	28/28	1		ENSP00000471242.1	C9JME2
STK24	ENST00000539966.6 linkuse as main transcript	c.*4880A>G		3_prime_UTR_variant	11/11	1	NM_001032296.4	ENSP00000442539.2	Q9Y6E0-2
FARP1	ENST00000627049.2 linkuse as main transcript	c.3207T>C	p.Ser1069Ser	synonymous_variant	28/28	5		ENSP00000486285.1	C9JME2

Frequencies

GnomAD3 genomes

AF:

0.542

AC:

82330

AN:

151980

Hom.:

22495

Cov.:

show subpopulations

Gnomad AFR

AF:

0.489

Gnomad AMI

AF:

0.651

Gnomad AMR

AF:

0.472

Gnomad ASJ

AF:

0.563

Gnomad EAS

AF:

0.568

Gnomad SAS

AF:

0.462

Gnomad FIN

AF:

0.633

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.577

Gnomad OTH

AF:

0.541

GnomAD3 exomes

AF:

0.538

AC:

135237

AN:

251400

Hom.:

37178

AF XY:

0.540

AC XY:

73349

AN XY:

135868

show subpopulations

Gnomad AFR exome

AF:

0.488

Gnomad AMR exome

AF:

0.403

Gnomad ASJ exome

AF:

0.558

Gnomad EAS exome

AF:

0.559

Gnomad SAS exome

AF:

0.459

Gnomad FIN exome

AF:

0.629

Gnomad NFE exome

AF:

0.583

Gnomad OTH exome

AF:

0.562

GnomAD4 exome

AF:

0.567

AC:

828766

AN:

1460532

Hom.:

237187

Cov.:

AF XY:

0.565

AC XY:

410292

AN XY:

726696

show subpopulations

Gnomad4 AFR exome

AF:

0.487

Gnomad4 AMR exome

AF:

0.414

Gnomad4 ASJ exome

AF:

0.559

Gnomad4 EAS exome

AF:

0.602

Gnomad4 SAS exome

AF:

0.462

Gnomad4 FIN exome

AF:

0.615

Gnomad4 NFE exome

AF:

0.581

Gnomad4 OTH exome

AF:

0.566

GnomAD4 genome

AF:

0.542

AC:

82381

AN:

152098

Hom.:

22512

Cov.:

AF XY:

0.542

AC XY:

40331

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.489

Gnomad4 AMR

AF:

0.471

Gnomad4 ASJ

AF:

0.563

Gnomad4 EAS

AF:

0.567

Gnomad4 SAS

AF:

0.461

Gnomad4 FIN

AF:

0.633

Gnomad4 NFE

AF:

0.577

Gnomad4 OTH

AF:

0.540

Alfa

AF:

0.566

Hom.:

40272

Bravo

AF:

0.530

Asia WGS

AF:

0.530

AC:

1840

AN:

3478

EpiCase

AF:

0.584

EpiControl

AF:

0.588

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

1.5

DANN

Benign

0.45

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over