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. Variant has been reported in ClinVar as (no stars).

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032389.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ARFGAP2	NM_032389.6	MANE Select	c.*609G>T	3_prime_UTR	Exon 16 of 16	NP_115765.2
ARFGAP2	NM_001410995.1		c.*609G>T	3_prime_UTR	Exon 17 of 17	NP_001397924.1	E9PN48
ARFGAP2	NM_001242832.2		c.*609G>T	3_prime_UTR	Exon 15 of 15	NP_001229761.1	G5E9L0

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ARFGAP2	ENST00000524782.6	TSL:1 MANE Select	c.*609G>T	3_prime_UTR	Exon 16 of 16	ENSP00000434442.1	Q8N6H7-1
ARFGAP2	ENST00000892878.1		c.*609G>T	3_prime_UTR	Exon 17 of 17	ENSP00000562937.1
ARFGAP2	ENST00000946556.1		c.*609G>T	3_prime_UTR	Exon 17 of 17	ENSP00000616615.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over