rs1476698

chr2-241357034-A-Gchr2-241357034-A-T

Variant summary

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

The NM_014808.4(FARP2):c.-25+646A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 152,134 control chromosomes in the GnomAD database, including 12,236 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 0.39 (12236 hom., cov: 33)
• Consequence: FARP2 NM_014808.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FARP2	NM_014808.4	c.-25+646A>G		intron_variant		ENST00000264042.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FARP2	ENST00000264042.8	c.-25+646A>G		intron_variant		1	NM_014808.4	P1

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59735 AN: 152016 Hom.: 12199 Cov.: 33

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.393 AC: 59829 AN: 152134 Hom.: 12236 Cov.: 33 AF XY: 0.397 AC XY: 29557 AN XY: 74368

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.404

Alfa AF: 0.361 Hom.: 7691

Bravo AF: 0.401

Asia WGS AF: 0.580 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.4
Dann	Benign	0.42

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: rs1476698; hg19: chr2-242296449;