rs9584805

Positions:

• chr13-98341776-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005766.4(FARP1):​c.172-1986A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,170 control chromosomes in the GnomAD database, including 8,902 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 0.33 (8902 hom., cov: 33)
• Consequence: FARP1 NM_005766.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FARP1	NM_005766.4	c.172-1986A>G		intron_variant		ENST00000319562.11	NP_005757.1
FARP1	NM_001286839.2	c.172-1986A>G		intron_variant			NP_001273768.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FARP1	ENST00000319562.11	c.172-1986A>G		intron_variant		1	NM_005766.4	ENSP00000322926.6

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49588 AN: 152052 Hom.: 8891 Cov.: 33

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.302

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.326 AC: 49636 AN: 152170 Hom.: 8902 Cov.: 33 AF XY: 0.316 AC XY: 23528 AN XY: 74374

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.0187

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.299

Alfa AF: 0.309 Hom.: 12068

Bravo AF: 0.325

Asia WGS AF: 0.143 AC: 500 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.0
DANN	Benign	0.46

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

Other links and lift over

dbSNP: rs9584805; hg19: chr13-98994030;