rs3821280

chr2-241395093-A-G

Variant summary

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

The NM_014808.4(FARP2):c.184-8735A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0894 in 152,208 control chromosomes in the GnomAD database, including 623 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 0.089 (623 hom., cov: 32)
• Consequence: FARP2 NM_014808.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

Genes affected

FARP2 (HGNC:16460): (FERM, ARH/RhoGEF and pleckstrin domain protein 2) Enables guanyl-nucleotide exchange factor activity. Acts upstream of or within Rac protein signal transduction and neuron remodeling. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FARP2	NM_014808.4	c.184-8735A>G		intron_variant		ENST00000264042.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FARP2	ENST00000264042.8	c.184-8735A>G		intron_variant		1	NM_014808.4	P1

Frequencies

GnomAD3 genomes AF: 0.0893 AC: 13583 AN: 152090 Hom.: 618 Cov.: 32

Gnomad AFR AF: 0.0900

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0793

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0950

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.0894 AC: 13602 AN: 152208 Hom.: 623 Cov.: 32 AF XY: 0.0893 AC XY: 6642 AN XY: 74420

Gnomad4 AFR AF: 0.0901

Gnomad4 AMR AF: 0.0665

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.0791

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0651

Gnomad4 NFE AF: 0.0950

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0961 Hom.: 333

Bravo AF: 0.0892

Asia WGS AF: 0.118 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.14
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: rs3821280; hg19: chr2-242334508;