Variant 15-72474873-T-TGGC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_005744.5(ARIH1):c.255_257dupCGG(p.Gly86dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0682 in 1,412,176 control chromosomes in the GnomAD database, including 2,491 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.057 ( 340 hom., cov: 32)

Exomes 𝑓: 0.070 ( 2151 hom. )

Consequence

ARIH1
NM_005744.5 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 2.74

Variant links:

Genes affected

ARIH1 (HGNC:689): (ariadne RBR E3 ubiquitin protein ligase 1) Enables enzyme binding activity; ubiquitin-protein transferase activity; and zinc ion binding activity. Involved in protein ubiquitination. Located in Lewy body; cytoplasm; and nuclear body. Colocalizes with cullin-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

ARIH1 links:

TMEM202-AS1 (HGNC:):

TMEM202-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 15-72474873-T-TGGC is Benign according to our data. Variant chr15-72474873-T-TGGC is described in ClinVar as [Benign]. Clinvar id is 402394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARIH1	NM_005744.5 linkuse as main transcript	c.255_257dupCGG	p.Gly86dup	disruptive_inframe_insertion	1/14	ENST00000379887.9	NP_005735.2	Q9Y4X5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ARIH1	ENST00000379887.9 linkuse as main transcript	c.255_257dupCGG	p.Gly86dup	disruptive_inframe_insertion	1/14	1	NM_005744.5	ENSP00000369217.4	Q9Y4X5
ARIH1	ENST00000564062.1 linkuse as main transcript	c.249_251dupCGG	p.Gly84dup	disruptive_inframe_insertion	1/4	3		ENSP00000454774.1	H3BNB9
TMEM202-AS1	ENST00000565181.1 linkuse as main transcript	n.293_295dupGCC		non_coding_transcript_exon_variant	1/1	6
ARIH1	ENST00000570085.5 linkuse as main transcript	n.255_257dupCGG		non_coding_transcript_exon_variant	1/5	3		ENSP00000456746.1	H3BSK4

Frequencies

GnomAD3 genomes

AF:

0.0569

AC:

8521

AN:

149668

Hom.:

338

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0133

Gnomad AMI

AF:

0.00337

Gnomad AMR

AF:

0.0545

Gnomad ASJ

AF:

0.0741

Gnomad EAS

AF:

0.000786

Gnomad SAS

AF:

0.0210

Gnomad FIN

AF:

0.120

Gnomad MID

AF:

0.0645

Gnomad NFE

AF:

0.0806

Gnomad OTH

AF:

0.0650

GnomAD3 exomes

AF:

0.0577

AC:

3555

AN:

61656

Hom.:

AF XY:

0.0549

AC XY:

1895

AN XY:

34494

show subpopulations

Gnomad AFR exome

AF:

0.00701

Gnomad AMR exome

AF:

0.0304

Gnomad ASJ exome

AF:

0.0662

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0213

Gnomad FIN exome

AF:

0.115

Gnomad NFE exome

AF:

0.0580

Gnomad OTH exome

AF:

0.0684

GnomAD4 exome

AF:

0.0696

AC:

87828

AN:

1262402

Hom.:

2151

Cov.:

AF XY:

0.0681

AC XY:

42151

AN XY:

619134

show subpopulations

Gnomad4 AFR exome

AF:

0.00980

Gnomad4 AMR exome

AF:

0.0311

Gnomad4 ASJ exome

AF:

0.0634

Gnomad4 EAS exome

AF:

0.000360

Gnomad4 SAS exome

AF:

0.0186

Gnomad4 FIN exome

AF:

0.111

Gnomad4 NFE exome

AF:

0.0757

Gnomad4 OTH exome

AF:

0.0608

GnomAD4 genome

AF:

0.0569

AC:

8528

AN:

149774

Hom.:

340

Cov.:

AF XY:

0.0586

AC XY:

4286

AN XY:

73138

show subpopulations

Gnomad4 AFR

AF:

0.0133

Gnomad4 AMR

AF:

0.0544

Gnomad4 ASJ

AF:

0.0741

Gnomad4 EAS

AF:

0.000788

Gnomad4 SAS

AF:

0.0223

Gnomad4 FIN

AF:

0.120

Gnomad4 NFE

AF:

0.0806

Gnomad4 OTH

AF:

0.0638

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

ARIH1-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 20, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over