chr2-241448569-A-G

Position:

• chr2-241448569-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.1411+7013A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,266 control chromosomes in the GnomAD database, including 3,087 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 0.19 (3087 hom., cov: 33)
• Consequence: FARP2 NM_014808.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

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 (NFE) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FARP2	NM_014808.4	c.1411+7013A>G		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+7013A>G		intron_variant		1	NM_014808.4	ENSP00000264042.3
FARP2	ENST00000373287.8	c.1411+7013A>G		intron_variant		1		ENSP00000362384.4
FARP2	ENST00000627550.2	c.1411+7013A>G		intron_variant		2		ENSP00000486597.1

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28892 AN: 152148 Hom.: 3089 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.190 AC: 28887 AN: 152266 Hom.: 3087 Cov.: 33 AF XY: 0.188 AC XY: 14028 AN XY: 74442

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0637

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.210

Alfa AF: 0.212 Hom.: 1846

Bravo AF: 0.189

Asia WGS AF: 0.0390 AC: 138 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	0.030
DANN	Benign	0.67

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: rs10192057; hg19: chr2-242387984;