rs1055447

Positions:

• chr11-47164873-C-A
• chr11-47164873-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032389.6(ARFGAP2):​c.*609G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,114 control chromosomes in the GnomAD database, including 20,513 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 0.52 (20486 hom., cov: 31)
  • Exomes 𝑓: 0.47 (27 hom.)
• Consequence: ARFGAP2 NM_032389.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARFGAP2	NM_032389.6	c.*609G>T		3_prime_UTR_variant	16/16	ENST00000524782.6	NP_115765.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARFGAP2	ENST00000524782	c.*609G>T		3_prime_UTR_variant	16/16	1	NM_032389.6	ENSP00000434442.1
ARFGAP2	ENST00000525314	c.*609G>T		3_prime_UTR_variant	17/17	3		ENSP00000434809.2
ARFGAP2	ENST00000426335	c.*609G>T		3_prime_UTR_variant	15/15	2		ENSP00000400226.3
ARFGAP2	ENST00000627920.2	c.*609G>T		3_prime_UTR_variant	11/11	2		ENSP00000486339.1

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78218 AN: 151794 Hom.: 20475 Cov.: 31

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.555

GnomAD4 exome AF: 0.465 AC: 94 AN: 202 Hom.: 27 Cov.: 0 AF XY: 0.426 AC XY: 52 AN XY: 122

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.750

Gnomad4 EAS exome AF: 0.625

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.477

Gnomad4 OTH exome AF: 0.455

GnomAD4 genome AF: 0.515 AC: 78259 AN: 151912 Hom.: 20486 Cov.: 31 AF XY: 0.513 AC XY: 38111 AN XY: 74258

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.562

Alfa AF: 0.522 Hom.: 10232

Bravo AF: 0.513

Asia WGS AF: 0.536 AC: 1864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	12
DANN	Benign	0.67
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs1055447; hg19: chr11-47186424;