2-241404918-A-G

Position:

• chr2-241404918-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.331+77A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,091,714 control chromosomes in the GnomAD database, including 6,080 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 0.10 (846 hom., cov: 33)
  • Exomes 𝑓: 0.10 (5234 hom.)
• Consequence: FARP2 NM_014808.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FARP2	NM_014808.4	c.331+77A>G		intron_variant		ENST00000264042.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FARP2	ENST00000264042.8	c.331+77A>G		intron_variant		1	NM_014808.4	P1

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15285 AN: 152106 Hom.: 844 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.0298

Gnomad SAS AF: 0.0753

Gnomad FIN AF: 0.0683

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0969

GnomAD4 exome AF: 0.104 AC: 97436 AN: 939490 Hom.: 5234 AF XY: 0.103 AC XY: 50354 AN XY: 487858

Gnomad4 AFR exome AF: 0.108

Gnomad4 AMR exome AF: 0.0996

Gnomad4 ASJ exome AF: 0.151

Gnomad4 EAS exome AF: 0.0506

Gnomad4 SAS exome AF: 0.0789

Gnomad4 FIN exome AF: 0.0767

Gnomad4 NFE exome AF: 0.110

Gnomad4 OTH exome AF: 0.101

GnomAD4 genome AF: 0.101 AC: 15299 AN: 152224 Hom.: 846 Cov.: 33 AF XY: 0.0975 AC XY: 7260 AN XY: 74426

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.0301

Gnomad4 SAS AF: 0.0756

Gnomad4 FIN AF: 0.0683

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0959

Alfa AF: 0.105 Hom.: 1167

Bravo AF: 0.101

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.91
DANN	Benign	0.26

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: rs11681497; hg19: chr2-242344333;