rs3821280

Variant names:

• chr2-241395093-A-G
• rs3821280
• NM_014808.4:c.184-8735A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FARP2	NM_014808.4	c.184-8735A>G		intron_variant	Intron 2 of 26	ENST00000264042.8	NP_055623.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FARP2	ENST00000264042.8	c.184-8735A>G		intron_variant	Intron 2 of 26	1	NM_014808.4	ENSP00000264042.3

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

African (AFR) AF: 0.0901 AC: 3741 AN: 41528

American (AMR) AF: 0.0665 AC: 1017 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 425 AN: 3468

East Asian (EAS) AF: 0.0791 AC: 409 AN: 5172

South Asian (SAS) AF: 0.117 AC: 563 AN: 4824

European-Finnish (FIN) AF: 0.0651 AC: 690 AN: 10600

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0950 AC: 6463 AN: 68000

Other (OTH) AF: 0.102 AC: 215 AN: 2112

Alfa AF: 0.0966 Hom.: 375

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
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3821280; hg19: chr2-242334508;