dbSNP rs11603334: ARAP1:c.-317C>T (chr11-72721940-G-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_001040118.3(ARAP1):c.509+4680C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 986,418 control chromosomes in the GnomAD database, including 11,210 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 0.12 ( 1404 hom., cov: 32)

Exomes 𝑓: 0.15 ( 9806 hom. )

Consequence

ARAP1
NM_001040118.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

Publications

101 publications found

Variant links:

Genes affected

ARAP1 (HGNC:16925): (ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1) The protein encoded by this gene contains SAM, ARF-GAP, RHO-GAP, ankyrin repeat, RAS-associating, and pleckstrin homology (PH) domains. In vitro, this protein displays RHO-GAP and phosphatidylinositol (3,4,5) trisphosphate (PIP3)-dependent ARF-GAP activity. The encoded protein associates with the Golgi, and the ARF-GAP activity mediates changes in the Golgi and the formation of filopodia. It is thought to regulate the cell-specific trafficking of a receptor protein involved in apoptosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]

ARAP1 links:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARAP1	NM_001040118.3 link	c.509+4680C>T		intron_variant	Intron 3 of 34	ENST00000393609.8	NP_001035207.1	Q96P48-6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARAP1	ENST00000393609.8 link	c.509+4680C>T		intron_variant	Intron 3 of 34	2	NM_001040118.3	ENSP00000377233.3		Q96P48-6

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18383

AN:

152104

Hom.:

1408

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0427

Gnomad AMI

AF:

0.128

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.0822

Gnomad EAS

AF:

0.0727

Gnomad SAS

AF:

0.185

Gnomad FIN

AF:

0.255

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.153

Gnomad OTH

AF:

0.0980

GnomAD4 exome

AF:

0.151

AC:

125813

AN:

834196

Hom.:

9806

Cov.:

AF XY:

0.152

AC XY:

58676

AN XY:

385240

show subpopulations

African (AFR)

AF:

0.0349

AC:

551

AN:

15804

American (AMR)

AF:

0.102

AC:

101

AN:

994

Ashkenazi Jewish (ASJ)

AF:

0.0877

AC:

454

AN:

5176

East Asian (EAS)

AF:

0.0574

AC:

216

AN:

3766

South Asian (SAS)

AF:

0.172

AC:

2834

AN:

16474

European-Finnish (FIN)

AF:

0.210

AC:

AN:

386

Middle Eastern (MID)

AF:

0.0844

AC:

137

AN:

1624

European-Non Finnish (NFE)

AF:

0.155

AC:

117996

AN:

762624

Other (OTH)

AF:

0.126

AC:

3443

AN:

27348

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

7614

15228

22841

30455

38069

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.121

AC:

18380

AN:

152222

Hom.:

1404

Cov.:

AF XY:

0.127

AC XY:

9419

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.0426

AC:

1771

AN:

41548

American (AMR)

AF:

0.104

AC:

1586

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0822

AC:

285

AN:

3468

East Asian (EAS)

AF:

0.0728

AC:

377

AN:

5176

South Asian (SAS)

AF:

0.184

AC:

888

AN:

4822

European-Finnish (FIN)

AF:

0.255

AC:

2697

AN:

10586

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.153

AC:

10435

AN:

67996

Other (OTH)

AF:

0.0984

AC:

208

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

846

1692

2538

3384

4230

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.133

Hom.:

6218

Bravo

AF:

0.104

Asia WGS

AF:

0.123

AC:

426

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.20

(source)

DANN

Benign

0.70

PhyloP100

-1.1

PromoterAI

0.0010

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=300/0

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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rs11603334

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