Variant 8-9011616-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_153332.4(ERI1):c.362A>G(p.Asn121Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00525 in 1,613,538 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0036 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0054 ( 32 hom. )

Consequence

ERI1
NM_153332.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.30

Variant links:

Genes affected

ERI1 (HGNC:23994): (exoribonuclease 1) Enables 3'-5' exonuclease activity. Predicted to be involved in exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Located in cytoplasm and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ERI1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0024873018).

BP6

Variant 8-9011616-A-G is Benign according to our data. Variant chr8-9011616-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3388034.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 32 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ERI1	NM_153332.4 linkuse as main transcript	c.362A>G	p.Asn121Ser	missense_variant	3/7	ENST00000250263.8	NP_699163.2	Q8IV48A0A024R355

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ERI1	ENST00000250263.8 linkuse as main transcript	c.362A>G	p.Asn121Ser	missense_variant	3/7	1	NM_153332.4	ENSP00000250263.7		Q8IV48

Frequencies

GnomAD3 genomes

AF:

0.00357

AC:

543

AN:

152180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00106

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00393

Gnomad ASJ

AF:

0.00230

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00217

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00590

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00346

AC:

868

AN:

251060

Hom.:

AF XY:

0.00340

AC XY:

461

AN XY:

135706

show subpopulations

Gnomad AFR exome

AF:

0.000800

Gnomad AMR exome

AF:

0.00220

Gnomad ASJ exome

AF:

0.00129

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000719

Gnomad FIN exome

AF:

0.00176

Gnomad NFE exome

AF:

0.00603

Gnomad OTH exome

AF:

0.00343

GnomAD4 exome

AF:

0.00543

AC:

7934

AN:

1461240

Hom.:

Cov.:

AF XY:

0.00527

AC XY:

3831

AN XY:

726920

show subpopulations

Gnomad4 AFR exome

AF:

0.000837

Gnomad4 AMR exome

AF:

0.00253

Gnomad4 ASJ exome

AF:

0.00176

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.000650

Gnomad4 FIN exome

AF:

0.00193

Gnomad4 NFE exome

AF:

0.00662

Gnomad4 OTH exome

AF:

0.00363

GnomAD4 genome

AF:

0.00357

AC:

544

AN:

152298

Hom.:

Cov.:

AF XY:

0.00350

AC XY:

261

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.00111

Gnomad4 AMR

AF:

0.00392

Gnomad4 ASJ

AF:

0.00230

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00217

Gnomad4 NFE

AF:

0.00588

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00420

Hom.:

Bravo

AF:

0.00362

TwinsUK

AF:

0.00782

AC:

ALSPAC

AF:

0.00830

AC:

ESP6500AA

AF:

0.000908

AC:

ESP6500EA

AF:

0.00488

AC:

ExAC

AF:

0.00364

AC:

442

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00487

EpiControl

AF:

0.00534

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2024

ERI1: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.056

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.0010

DANN

Benign

0.55

DEOGEN2

Benign

0.064

T;T;T

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.11

LIST_S2

Benign

0.47

.;T;.

M_CAP

Benign

0.0032

MetaRNN

Benign

0.0025

T;T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

-1.0

N;N;N

PrimateAI

Benign

0.29

PROVEAN

Benign

-0.21

N;N;N

REVEL

Benign

0.031

Sift

Benign

0.71

T;T;T

Sift4G

Benign

0.84

T;T;T

Polyphen

0.0

B;B;B

Vest4

0.038

MVP

0.055

MPC

0.0076

ClinPred

0.0028

GERP RS

-5.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.064

gMVP

0.24

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

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