2-241440380-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014808.4(FARP2):​c.1159-924G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,176 control chromosomes in the GnomAD database, including 2,519 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 0.17 (2519 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014808.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FARP2	NM_014808.4	MANE Select	c.1159-924G>T		intron	N/A	NP_055623.1
	FARP2	NM_001282983.2		c.1159-924G>T		intron	N/A	NP_001269912.1
	FARP2	NM_001282984.2		c.1159-924G>T		intron	N/A	NP_001269913.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FARP2	ENST00000264042.8	TSL:1 MANE Select	c.1159-924G>T		intron	N/A	ENSP00000264042.3
	FARP2	ENST00000373287.8	TSL:1	c.1159-924G>T		intron	N/A	ENSP00000362384.4
	FARP2	ENST00000627550.2	TSL:2	c.1159-924G>T		intron	N/A	ENSP00000486597.1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25422 AN: 152058 Hom.: 2518 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.167 AC: 25439 AN: 152176 Hom.: 2519 Cov.: 32 AF XY: 0.171 AC XY: 12744 AN XY: 74388

African (AFR) AF: 0.102 AC: 4229 AN: 41536

American (AMR) AF: 0.123 AC: 1883 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3472

East Asian (EAS) AF: 0.403 AC: 2082 AN: 5164

South Asian (SAS) AF: 0.245 AC: 1181 AN: 4820

European-Finnish (FIN) AF: 0.259 AC: 2738 AN: 10572

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12387 AN: 68002

Other (OTH) AF: 0.150 AC: 317 AN: 2114

Alfa AF: 0.167 Hom.: 372

Bravo AF: 0.154

Asia WGS AF: 0.299 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.62
PhyloP100		0.032
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: rs3755400; hg19: chr2-242379795;