rs3771570

Positions:

• chr2-241443449-C-T

Variant summary

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

The NM_014808.4(FARP2):​c.1411+1893C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,516 control chromosomes in the GnomAD database, including 1,192 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 0.11 (1191 hom., cov: 33)
  • Exomes 𝑓: 0.079 (1 hom.)
• Consequence: FARP2 NM_014808.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FARP2	NM_014808.4	c.1411+1893C>T		intron_variant		ENST00000264042.8	NP_055623.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FARP2	ENST00000264042.8	c.1411+1893C>T		intron_variant		1	NM_014808.4	ENSP00000264042.3
FARP2	ENST00000373287.8	c.1411+1893C>T		intron_variant		1		ENSP00000362384.4
FARP2	ENST00000413432.2	c.*916C>T		3_prime_UTR_variant	4/4	2		ENSP00000412772.2
FARP2	ENST00000627550.2	c.1411+1893C>T		intron_variant		2		ENSP00000486597.1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16820 AN: 152158 Hom.: 1192 Cov.: 33

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.0792 AC: 19 AN: 240 Hom.: 1 Cov.: 0 AF XY: 0.0633 AC XY: 10 AN XY: 158

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0938

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0706

Gnomad4 OTH exome AF: 0.188

GnomAD4 genome AF: 0.110 AC: 16813 AN: 152276 Hom.: 1191 Cov.: 33 AF XY: 0.108 AC XY: 8062 AN XY: 74456

Gnomad4 AFR AF: 0.0301

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.129

Alfa AF: 0.138 Hom.: 900

Bravo AF: 0.107

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.69

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: rs3771570; hg19: chr2-242382864;