dbSNP rs1055447: ARFGAP2:c.*609G>T (chr11-47164873-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.17

Publications

22 publications found

Variant links:

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]

ARFGAP2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ARFGAP2	NM_032389.6 link	c.*609G>T		3_prime_UTR_variant	Exon 16 of 16	ENST00000524782.6	NP_115765.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
ARFGAP2	ENST00000524782.6 link	c.*609G>T	3_prime_UTR_variant	Exon 16 of 16	1	NM_032389.6	ENSP00000434442.1
ARFGAP2	ENST00000525314.6 link	c.*609G>T	3_prime_UTR_variant	Exon 17 of 17	3		ENSP00000434809.2
ARFGAP2	ENST00000426335.6 link	c.*609G>T	3_prime_UTR_variant	Exon 15 of 15	2		ENSP00000400226.3
ARFGAP2	ENST00000627920.2 link	c.*609G>T	3_prime_UTR_variant	Exon 11 of 11	2		ENSP00000486339.1

Frequencies

GnomAD3 genomes

AF:

0.515

AC:

78218

AN:

151794

Hom.:

20475

Cov.:

show subpopulations

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:

AN:

202

Hom.:

Cov.:

AF XY:

0.426

AC XY:

AN XY:

122

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

AN:

East Asian (EAS)

AF:

0.625

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.477

AC:

AN:

128

Other (OTH)

AF:

0.455

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.515

AC:

78259

AN:

151912

Hom.:

20486

Cov.:

AF XY:

0.513

AC XY:

38111

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.505

AC:

20911

AN:

41408

American (AMR)

AF:

0.514

AC:

7850

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.588

AC:

2036

AN:

3462

East Asian (EAS)

AF:

0.286

AC:

1478

AN:

5162

South Asian (SAS)

AF:

0.643

AC:

3089

AN:

4804

European-Finnish (FIN)

AF:

0.454

AC:

4799

AN:

10578

Middle Eastern (MID)

AF:

0.605

AC:

178

AN:

294

European-Non Finnish (NFE)

AF:

0.533

AC:

36193

AN:

67920

Other (OTH)

AF:

0.562

AC:

1183

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1943

3886

5830

7773

9716

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

690

1380

2070

2760

3450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.524

Hom.:

11479

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

(source)

DANN

Benign

0.67

PhyloP100

1.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over