Variant 9-95876006-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_020207.7(ERCC6L2):c.-33A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 1,570,194 control chromosomes in the GnomAD database, including 73,488 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5846 hom., cov: 33)

Exomes 𝑓: 0.31 ( 67642 hom. )

Consequence

ERCC6L2
NM_020207.7 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0600

Variant links:

Genes affected

ERCC6L2 (HGNC:26922): (ERCC excision repair 6 like 2) This gene encodes a member of the Snf2 family of helicase-like proteins. The encoded protein may play a role in DNA repair and mitochondrial function. Mutations in this gene have been associated with bone marrow failure syndrome 2. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Apr 2014]

ERCC6L2 links:

ERCC6L2-AS1 (HGNC:27858): (ERCC6L2 antisense RNA 1)

ERCC6L2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=8.9636445E-4).

BP6

Variant 9-95876006-A-G is Benign according to our data. Variant chr9-95876006-A-G is described in ClinVar as [Benign]. Clinvar id is 1165173.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERCC6L2	NM_020207.7 link	c.-33A>G		5_prime_UTR_variant	Exon 1 of 19	ENST00000653738.2	NP_064592.3	Q5T890

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ERCC6L2	ENST00000653738 link	c.-33A>G		5_prime_UTR_variant	Exon 1 of 19		NM_020207.7	ENSP00000499221.2		A0A590UJ07

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39914

AN:

152046

Hom.:

5849

Cov.:

show subpopulations

Gnomad AFR

AF:

0.130

Gnomad AMI

AF:

0.432

Gnomad AMR

AF:

0.307

Gnomad ASJ

AF:

0.374

Gnomad EAS

AF:

0.371

Gnomad SAS

AF:

0.273

Gnomad FIN

AF:

0.277

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.313

Gnomad OTH

AF:

0.276

GnomAD3 exomes

AF:

0.301

AC:

54955

AN:

182664

Hom.:

8400

AF XY:

0.301

AC XY:

29837

AN XY:

99156

show subpopulations

Gnomad AFR exome

AF:

0.118

Gnomad AMR exome

AF:

0.328

Gnomad ASJ exome

AF:

0.385

Gnomad EAS exome

AF:

0.382

Gnomad SAS exome

AF:

0.272

Gnomad FIN exome

AF:

0.264

Gnomad NFE exome

AF:

0.307

Gnomad OTH exome

AF:

0.305

GnomAD4 exome

AF:

0.307

AC:

435022

AN:

1418030

Hom.:

67642

Cov.:

AF XY:

0.307

AC XY:

215035

AN XY:

701538

show subpopulations

Gnomad4 AFR exome

AF:

0.119

Gnomad4 AMR exome

AF:

0.322

Gnomad4 ASJ exome

AF:

0.385

Gnomad4 EAS exome

AF:

0.338

Gnomad4 SAS exome

AF:

0.272

Gnomad4 FIN exome

AF:

0.266

Gnomad4 NFE exome

AF:

0.314

Gnomad4 OTH exome

AF:

0.296

GnomAD4 genome

AF:

0.262

AC:

39916

AN:

152164

Hom.:

5846

Cov.:

AF XY:

0.265

AC XY:

19702

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.130

Gnomad4 AMR

AF:

0.307

Gnomad4 ASJ

AF:

0.374

Gnomad4 EAS

AF:

0.370

Gnomad4 SAS

AF:

0.274

Gnomad4 FIN

AF:

0.277

Gnomad4 NFE

AF:

0.313

Gnomad4 OTH

AF:

0.273

Alfa

AF:

0.301

Hom.:

3806

Bravo

AF:

0.258

TwinsUK

AF:

0.314

AC:

1165

ALSPAC

AF:

0.321

AC:

1237

ESP6500AA

AF:

0.131

AC:

561

ESP6500EA

AF:

0.298

AC:

2502

ExAC

AF:

0.244

AC:

28272

Asia WGS

AF:

0.273

AC:

946

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Dec 02, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.39

CADD

Benign

9.8

DANN

Benign

0.43

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.00091

LIST_S2

Uncertain

0.90

MetaRNN

Benign

0.00090

MetaSVM

Benign

-1.1

PROVEAN

Benign

0.31

REVEL

Benign

0.23

Sift

Benign

1.0

Sift4G

Pathogenic

0.0

Vest4

0.021

ClinPred

0.0047

GERP RS

-3.7

gMVP

0.20

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