13-98174781-G-C

Position:

• chr13-98174781-G-C

Variant summary

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

The NM_005766.4(FARP1):​c.-24+31289G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,928 control chromosomes in the GnomAD database, including 25,278 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 (25278 hom., cov: 32)
• Consequence: FARP1 NM_005766.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48

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]

ACMG classification

Verdict is Benign. Variant got -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 = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FARP1	NM_005766.4	c.-24+31289G>C		intron_variant		ENST00000319562.11
FARP1	NM_001001715.4	c.-24+31289G>C		intron_variant
FARP1	NM_001286839.2	c.-24+32004G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FARP1	ENST00000319562.11	c.-24+31289G>C		intron_variant		1	NM_005766.4	P1

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82157 AN: 151810 Hom.: 25282 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.541 AC: 82162 AN: 151928 Hom.: 25278 Cov.: 32 AF XY: 0.541 AC XY: 40157 AN XY: 74236

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.564

Alfa AF: 0.586 Hom.: 3485

Bravo AF: 0.526

Asia WGS AF: 0.689 AC: 2396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.042
DANN	Benign	0.47

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: rs285098; hg19: chr13-98827035;