dbSNP rs757131763: ARHGDIA:c.*65delC (chr17-81868810-TG-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_004309.6(ARHGDIA):c.*65delC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00029 in 437,590 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00017 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00030 ( 1 hom. )

Consequence

ARHGDIA
NM_004309.6 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0640

Publications

0 publications found

Variant links:

Genes affected

ARHGDIA (HGNC:678): (Rho GDP dissociation inhibitor alpha) This gene encodes a protein that plays a key role in the regulation of signaling through Rho GTPases. The encoded protein inhibits the disassociation of Rho family members from GDP (guanine diphosphate), thereby maintaining these factors in an inactive state. Activity of this protein is important in a variety of cellular processes, and expression of this gene may be altered in tumors. Mutations in this gene have been found in individuals with nephrotic syndrome, type 8. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

ARHGDIA Gene-Disease associations (from GenCC):

nephrotic syndrome, type 8
Inheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
familial idiopathic steroid-resistant nephrotic syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ARHGDIA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004309.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
ARHGDIA	NM_004309.6	MANE Select	c.*65delC		3_prime_UTR	Exon 6 of 6	NP_004300.1
ARHGDIA	NM_001301242.2		c.568delC	p.Gln190SerfsTer144	frameshift	Exon 7 of 7	NP_001288171.1
ARHGDIA	NR_125441.2		n.670delC		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
ARHGDIA	ENST00000269321.12	TSL:1 MANE Select	c.*65delC		3_prime_UTR	Exon 6 of 6	ENSP00000269321.7
ARHGDIA	ENST00000580685.5	TSL:1	c.*65delC		3_prime_UTR	Exon 5 of 5	ENSP00000464205.1
ARHGDIA	ENST00000583868.5	TSL:3	c.568delC	p.Gln190SerfsTer60	frameshift	Exon 7 of 7	ENSP00000462209.1

Frequencies

GnomAD3 genomes

AF:

0.000171

AC:

AN:

40934

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000475

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000496

Gnomad SAS

AF:

0.000740

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000221

AC:

AN:

204026

AF XY:

0.000249

show subpopulations

Gnomad AFR exome

AF:

0.000152

Gnomad AMR exome

AF:

0.000309

Gnomad ASJ exome

AF:

0.000119

Gnomad EAS exome

AF:

0.000738

Gnomad FIN exome

AF:

0.0000531

Gnomad NFE exome

AF:

0.0000319

Gnomad OTH exome

AF:

0.000208

GnomAD4 exome

AF:

0.000303

AC:

120

AN:

396596

Hom.:

Cov.:

AF XY:

0.000365

AC XY:

AN XY:

216660

show subpopulations

African (AFR)

AF:

0.000435

AC:

AN:

11490

American (AMR)

AF:

0.000309

AC:

AN:

29102

Ashkenazi Jewish (ASJ)

AF:

0.0000945

AC:

AN:

10584

East Asian (EAS)

AF:

0.00146

AC:

AN:

11652

South Asian (SAS)

AF:

0.00101

AC:

AN:

49554

European-Finnish (FIN)

AF:

0.0000401

AC:

AN:

24942

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2704

European-Non Finnish (NFE)

AF:

0.000125

AC:

AN:

240010

Other (OTH)

AF:

0.000423

AC:

AN:

16558

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

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:

0.000171

AC:

AN:

40994

Hom.:

Cov.:

AF XY:

0.0000494

AC XY:

AN XY:

20260

show subpopulations

African (AFR)

AF:

0.000473

AC:

AN:

10574

American (AMR)

AF:

0.00

AC:

AN:

3814

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

990

East Asian (EAS)

AF:

0.000496

AC:

AN:

2016

South Asian (SAS)

AF:

0.000739

AC:

AN:

1354

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2084

Middle Eastern (MID)

AF:

0.00

AC:

AN:

150

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

19224

Other (OTH)

AF:

0.00

AC:

AN:

550

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

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

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.064

Mutation Taster

=100/0

polymorphism

(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