rs11681497

Variant names:

• chr2-241404918-A-G
• rs11681497
• NM_014808.4:c.331+77A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-241404918-A-G
• chr2-241404918-A-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.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
• Publications: 29 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FARP2	NM_014808.4	MANE Select	c.331+77A>G		intron	N/A	NP_055623.1	O94887-1
	FARP2	NM_001282983.2		c.331+77A>G		intron	N/A	NP_001269912.1	O94887-2
	FARP2	NM_001282984.2		c.331+77A>G		intron	N/A	NP_001269913.1	O94887-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FARP2	ENST00000264042.8	TSL:1 MANE Select	c.331+77A>G		intron	N/A	ENSP00000264042.3	O94887-1
	FARP2	ENST00000373287.8	TSL:1	c.331+77A>G		intron	N/A	ENSP00000362384.4	O94887-2
	FARP2	ENST00000903053.1		c.331+77A>G		intron	N/A	ENSP00000573112.1

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

African (AFR) AF: 0.108 AC: 2554 AN: 23566

American (AMR) AF: 0.0996 AC: 4251 AN: 42678

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 3370 AN: 22256

East Asian (EAS) AF: 0.0506 AC: 1880 AN: 37174

South Asian (SAS) AF: 0.0789 AC: 5804 AN: 73576

European-Finnish (FIN) AF: 0.0767 AC: 3908 AN: 50928

Middle Eastern (MID) AF: 0.124 AC: 584 AN: 4698

European-Non Finnish (NFE) AF: 0.110 AC: 70753 AN: 641616

Other (OTH) AF: 0.101 AC: 4332 AN: 42998

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

African (AFR) AF: 0.102 AC: 4256 AN: 41532

American (AMR) AF: 0.104 AC: 1589 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 546 AN: 3470

East Asian (EAS) AF: 0.0301 AC: 156 AN: 5188

South Asian (SAS) AF: 0.0756 AC: 364 AN: 4816

European-Finnish (FIN) AF: 0.0683 AC: 724 AN: 10604

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7361 AN: 67994

Other (OTH) AF: 0.0959 AC: 203 AN: 2116

Alfa AF: 0.105 Hom.: 1491

Bravo AF: 0.101

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.91
DANN	Benign	0.26
PhyloP100		-0.30
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: rs11681497; hg19: chr2-242344333; COSMIC: COSV107247811; COSMIC: COSV107247811;