rs3755400

Variant names:

• chr2-241440380-G-C
• rs3755400
• NM_014808.4:c.1159-924G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-241440380-G-C
• chr2-241440380-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014808.4(FARP2):​c.1159-924G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: FARP2 NM_014808.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 6 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FARP2	NM_014808.4	c.1159-924G>C		intron_variant	Intron 12 of 26	ENST00000264042.8	NP_055623.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FARP2	ENST00000264042.8	c.1159-924G>C		intron_variant	Intron 12 of 26	1	NM_014808.4	ENSP00000264042.3
FARP2	ENST00000373287.8	c.1159-924G>C		intron_variant	Intron 12 of 17	1		ENSP00000362384.4
FARP2	ENST00000627550.2	c.1159-924G>C		intron_variant	Intron 12 of 17	2		ENSP00000486597.1
FARP2	ENST00000413432.2	c.220-924G>C		intron_variant	Intron 3 of 3	2		ENSP00000412772.2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		0.032

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: rs3755400; hg19: chr2-242379795;