Variant chr9-95876024-C-T 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.-15C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0943 in 1,584,238 control chromosomes in the GnomAD database, including 8,015 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.086 ( 753 hom., cov: 32)

Exomes 𝑓: 0.095 ( 7262 hom. )

Consequence

ERCC6L2
NM_020207.7 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.20

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=0.00238809).

BP6

Variant 9-95876024-C-T is Benign according to our data. Variant chr9-95876024-C-T is described in ClinVar as [Benign]. Clinvar id is 1169826.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERCC6L2	NM_020207.7 linkuse as main transcript	c.-15C>T		5_prime_UTR_variant	1/19	ENST00000653738.2
ERCC6L2-AS1	NR_023390.1 linkuse as main transcript			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERCC6L2	ENST00000653738.2 linkuse as main transcript	c.-15C>T		5_prime_UTR_variant	1/19		NM_020207.7	P2

Frequencies

GnomAD3 genomes

AF:

0.0860

AC:

13082

AN:

152174

Hom.:

750

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0343

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.135

Gnomad ASJ

AF:

0.0607

Gnomad EAS

AF:

0.165

Gnomad SAS

AF:

0.0923

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0909

Gnomad OTH

AF:

0.0898

GnomAD3 exomes

AF:

0.115

AC:

22915

AN:

199718

Hom.:

1595

AF XY:

0.110

AC XY:

11944

AN XY:

108922

show subpopulations

Gnomad AFR exome

AF:

0.0318

Gnomad AMR exome

AF:

0.194

Gnomad ASJ exome

AF:

0.0635

Gnomad EAS exome

AF:

0.165

Gnomad SAS exome

AF:

0.0938

Gnomad FIN exome

AF:

0.164

Gnomad NFE exome

AF:

0.0913

Gnomad OTH exome

AF:

0.106

GnomAD4 exome

AF:

0.0952

AC:

136360

AN:

1431946

Hom.:

7262

Cov.:

AF XY:

0.0949

AC XY:

67368

AN XY:

709878

show subpopulations

Gnomad4 AFR exome

AF:

0.0316

Gnomad4 AMR exome

AF:

0.188

Gnomad4 ASJ exome

AF:

0.0623

Gnomad4 EAS exome

AF:

0.171

Gnomad4 SAS exome

AF:

0.0934

Gnomad4 FIN exome

AF:

0.160

Gnomad4 NFE exome

AF:

0.0897

Gnomad4 OTH exome

AF:

0.0867

GnomAD4 genome

AF:

0.0860

AC:

13092

AN:

152292

Hom.:

753

Cov.:

AF XY:

0.0905

AC XY:

6739

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.0342

Gnomad4 AMR

AF:

0.135

Gnomad4 ASJ

AF:

0.0607

Gnomad4 EAS

AF:

0.165

Gnomad4 SAS

AF:

0.0928

Gnomad4 FIN

AF:

0.160

Gnomad4 NFE

AF:

0.0909

Gnomad4 OTH

AF:

0.0888

Alfa

AF:

0.0868

Hom.:

543

Bravo

AF:

0.0836

TwinsUK

AF:

0.0863

AC:

320

ALSPAC

AF:

0.0903

AC:

348

ESP6500AA

AF:

0.0267

AC:

115

ESP6500EA

AF:

0.0851

AC:

721

ExAC

AF:

0.0956

AC:

11354

Asia WGS

AF:

0.118

AC:

409

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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

BayesDel_addAF

Benign

-0.34

BayesDel_noAF

Benign

-0.12

CADD

Benign

DANN

Uncertain

1.0

Eigen

Benign

-0.66

Eigen_PC

Benign

-0.69

FATHMM_MKL

Benign

0.0076

LIST_S2

Benign

0.45

MetaRNN

Benign

0.0024

MetaSVM

Benign

-0.90

MutationTaster

Benign

1.0

PrimateAI

Benign

0.42

PROVEAN

Benign

-0.24

REVEL

Benign

0.13

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Vest4

0.13

MPC

0.25

ClinPred

0.12

GERP RS

3.2

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