rs755766412

Variant names:

• chr11-47166879-T-C
• rs755766412
• NM_032389.6:c.1213A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-47166879-T-C
• chr11-47166879-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_032389.6(ARFGAP2):​c.1213A>G​(p.Asn405Asp) variant causes a missense 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. 14/21 in silico tools predict 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: 33)
• Consequence: ARFGAP2 NM_032389.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68

Genes affected

ARFGAP2 (HGNC:13504): (ADP ribosylation factor GTPase activating protein 2) Predicted to enable GTPase activator activity. Predicted to be involved in COPI coating of Golgi vesicle. Located in Golgi apparatus; cytosol; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.1100446).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARFGAP2	NM_032389.6	c.1213A>G	p.Asn405Asp	missense_variant	Exon 13 of 16	ENST00000524782.6	NP_115765.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARFGAP2	ENST00000524782.6	c.1213A>G	p.Asn405Asp	missense_variant	Exon 13 of 16	1	NM_032389.6	ENSP00000434442.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	20
DANN	Uncertain	0.99
DEOGEN2	Benign	0.030	.;T;T;.;.
Eigen	Benign	-0.19
Eigen_PC	Benign	-0.059
FATHMM_MKL	Benign	0.67	D
LIST_S2	Uncertain	0.86	D;D;D;D;D
M_CAP	Benign	0.0073	T
MetaRNN	Benign	0.11	T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.7	.;.;L;.;.
PrimateAI	Benign	0.35	T
PROVEAN	Benign	-0.99	.;.;N;N;N
REVEL	Benign	0.11
Sift	Benign	0.55	.;.;T;D;D
Sift4G	Benign	0.49	T;T;T;T;.
Polyphen		0.053	.;.;B;.;.
Vest4		0.23
MutPred		0.18		.;.;Loss of MoRF binding (P = 0.0425);.;.;
MVP		0.24
MPC		0.30
ClinPred		0.32	T
GERP RS		5.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.13
gMVP		0.13

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs755766412; hg19: chr11-47188430;