17-81868810-TG-TGGGGGGG

Variant names:

• chr17-81868810-T-TGGGGGG
• rs757131763
• NM_004309.6:c.*60_*65dupCCCCCC

Variant summary

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

The NM_004309.6(ARHGDIA):​c.*60_*65dupCCCCCC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ARHGDIA NM_004309.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 0 publications found

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

ACMG classification

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARHGDIA	NM_004309.6	c.*60_*65dupCCCCCC		3_prime_UTR_variant	Exon 6 of 6	ENST00000269321.12	NP_004300.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARHGDIA	ENST00000269321.12	c.*60_*65dupCCCCCC		3_prime_UTR_variant	Exon 6 of 6	1	NM_004309.6	ENSP00000269321.7

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 40932 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 396948 Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0 AN XY: 216816

African (AFR) AF: 0.00 AC: 0 AN: 11504

American (AMR) AF: 0.00 AC: 0 AN: 29104

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10586

East Asian (EAS) AF: 0.00 AC: 0 AN: 11658

South Asian (SAS) AF: 0.00 AC: 0 AN: 49562

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24972

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2704

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 240296

Other (OTH) AF: 0.00 AC: 0 AN: 16562

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 40932 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 20206

African (AFR) AF: 0.00 AC: 0 AN: 10526

American (AMR) AF: 0.00 AC: 0 AN: 3798

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 990

East Asian (EAS) AF: 0.00 AC: 0 AN: 2018

South Asian (SAS) AF: 0.00 AC: 0 AN: 1352

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2084

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 164

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 19222

Other (OTH) AF: 0.00 AC: 0 AN: 540

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.064
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs757131763; hg19: chr17-79826686;