Variant rs8481 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005766.4(FARP1):c.*4824G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 1,610,474 control chromosomes in the GnomAD database, including 62,742 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 0.26 ( 5217 hom., cov: 32)

Exomes 𝑓: 0.28 ( 57525 hom. )

Consequence

FARP1
NM_005766.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0940

Variant links:

Genes affected

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:

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK24	NM_001032296.4 linkuse as main transcript	c.*32C>T		3_prime_UTR_variant	11/11	ENST00000539966.6
FARP1	NM_005766.4 linkuse as main transcript	c.*4824G>A		3_prime_UTR_variant	27/27	ENST00000319562.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FARP1	ENST00000319562.11 linkuse as main transcript	c.*4824G>A		3_prime_UTR_variant	27/27	1	NM_005766.4	P1	Q9Y4F1-1
STK24	ENST00000539966.6 linkuse as main transcript	c.*32C>T		3_prime_UTR_variant	11/11	1	NM_001032296.4	P1	Q9Y6E0-2

Frequencies

GnomAD3 genomes

AF:

0.259

AC:

39265

AN:

151804

Hom.:

5206

Cov.:

show subpopulations

Gnomad AFR

AF:

0.227

Gnomad AMI

AF:

0.316

Gnomad AMR

AF:

0.242

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.213

Gnomad FIN

AF:

0.226

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.297

Gnomad OTH

AF:

0.258

GnomAD3 exomes

AF:

0.252

AC:

62844

AN:

249726

Hom.:

8222

AF XY:

0.253

AC XY:

34207

AN XY:

135092

show subpopulations

Gnomad AFR exome

AF:

0.228

Gnomad AMR exome

AF:

0.217

Gnomad ASJ exome

AF:

0.260

Gnomad EAS exome

AF:

0.159

Gnomad SAS exome

AF:

0.227

Gnomad FIN exome

AF:

0.235

Gnomad NFE exome

AF:

0.290

Gnomad OTH exome

AF:

0.244

GnomAD4 exome

AF:

0.277

AC:

404655

AN:

1458552

Hom.:

57525

Cov.:

AF XY:

0.277

AC XY:

200727

AN XY:

725750

show subpopulations

Gnomad4 AFR exome

AF:

0.224

Gnomad4 AMR exome

AF:

0.218

Gnomad4 ASJ exome

AF:

0.261

Gnomad4 EAS exome

AF:

0.145

Gnomad4 SAS exome

AF:

0.230

Gnomad4 FIN exome

AF:

0.245

Gnomad4 NFE exome

AF:

0.293

Gnomad4 OTH exome

AF:

0.264

GnomAD4 genome

AF:

0.259

AC:

39301

AN:

151922

Hom.:

5217

Cov.:

AF XY:

0.254

AC XY:

18856

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.227

Gnomad4 AMR

AF:

0.242

Gnomad4 ASJ

AF:

0.256

Gnomad4 EAS

AF:

0.154

Gnomad4 SAS

AF:

0.214

Gnomad4 FIN

AF:

0.226

Gnomad4 NFE

AF:

0.297

Gnomad4 OTH

AF:

0.257

Alfa

AF:

0.242

Hom.:

1233

Bravo

AF:

0.256

Asia WGS

AF:

0.192

AC:

670

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.0

DANN

Benign

0.58

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