10-49530735-T-C

Position:

chr10-49530735-T-C

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000355832.10(ERCC6):c.528A>G(p.Arg176Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0137 in 1,613,584 control chromosomes in the GnomAD database, including 660 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. R176R) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.016 ( 59 hom., cov: 32)

Exomes 𝑓: 0.013 ( 601 hom. )

Consequence

ERCC6
ENST00000355832.10 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: -0.0750

Variant links:

Genes affected

ERCC6 (HGNC:3438): (ERCC excision repair 6, chromatin remodeling factor) This gene encodes a DNA-binding protein that is important in transcription-coupled excision repair. The encoded protein has ATP-stimulated ATPase activity, interacts with several transcription and excision repair proteins, and may promote complex formation at DNA repair sites. Mutations in this gene are associated with Cockayne syndrome type B and cerebrooculofacioskeletal syndrome 1. Alternative splicing occurs between a splice site from exon 5 of this gene to the 3' splice site upstream of the open reading frame (ORF) of the adjacent gene, piggyback-derived-3 (GeneID:267004), which activates the alternative polyadenylation site downstream of the piggyback-derived-3 ORF. The resulting transcripts encode a fusion protein that shares sequence with the product of each individual gene. [provided by RefSeq, Mar 2016]

ERCC6 links:

ERCC6 (HGNC:):

ERCC6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 10-49530735-T-C is Benign according to our data. Variant chr10-49530735-T-C is described in ClinVar as [Benign]. Clinvar id is 196213.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-49530735-T-C is described in Lovd as [Likely_benign]. Variant chr10-49530735-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.075 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ERCC6	NM_000124.4 linkuse as main transcript	c.528A>G	p.Arg176Arg	synonymous_variant	3/21	ENST00000355832.10	NP_000115.1	Q03468-1Q59FF6
ERCC6	NM_001277058.2 linkuse as main transcript	c.528A>G	p.Arg176Arg	synonymous_variant	3/6	ENST00000447839.7	NP_001263987.1	P0DP91-1A8K4Q3
ERCC6	NM_001346440.2 linkuse as main transcript	c.528A>G	p.Arg176Arg	synonymous_variant	3/21		NP_001333369.1	Q03468-1
ERCC6	NM_001277059.2 linkuse as main transcript	c.528A>G	p.Arg176Arg	synonymous_variant	3/6		NP_001263988.1	P0DP91-1A8K4Q3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ERCC6	ENST00000355832.10 linkuse as main transcript	c.528A>G	p.Arg176Arg	synonymous_variant	3/21	1	NM_000124.4	ENSP00000348089.5		Q03468-1
ERCC6	ENST00000447839.7 linkuse as main transcript	c.528A>G	p.Arg176Arg	synonymous_variant	3/6	2	NM_001277058.2	ENSP00000387966.2		P0DP91-1

Frequencies

GnomAD3 genomes

AF:

0.0155

AC:

2362

AN:

152200

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00270

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0683

Gnomad ASJ

AF:

0.00461

Gnomad EAS

AF:

0.0514

Gnomad SAS

AF:

0.00807

Gnomad FIN

AF:

0.0297

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00788

Gnomad OTH

AF:

0.0153

GnomAD3 exomes

AF:

0.0287

AC:

7219

AN:

251258

Hom.:

392

AF XY:

0.0237

AC XY:

3225

AN XY:

135820

show subpopulations

Gnomad AFR exome

AF:

0.00289

Gnomad AMR exome

AF:

0.132

Gnomad ASJ exome

AF:

0.00496

Gnomad EAS exome

AF:

0.0467

Gnomad SAS exome

AF:

0.00379

Gnomad FIN exome

AF:

0.0267

Gnomad NFE exome

AF:

0.00797

Gnomad OTH exome

AF:

0.0191

GnomAD4 exome

AF:

0.0135

AC:

19688

AN:

1461266

Hom.:

601

Cov.:

AF XY:

0.0127

AC XY:

9203

AN XY:

726946

show subpopulations

Gnomad4 AFR exome

AF:

0.00239

Gnomad4 AMR exome

AF:

0.126

Gnomad4 ASJ exome

AF:

0.00517

Gnomad4 EAS exome

AF:

0.0595

Gnomad4 SAS exome

AF:

0.00437

Gnomad4 FIN exome

AF:

0.0241

Gnomad4 NFE exome

AF:

0.00808

Gnomad4 OTH exome

AF:

0.0135

GnomAD4 genome

AF:

0.0155

AC:

2366

AN:

152318

Hom.:

Cov.:

AF XY:

0.0175

AC XY:

1300

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.00269

Gnomad4 AMR

AF:

0.0684

Gnomad4 ASJ

AF:

0.00461

Gnomad4 EAS

AF:

0.0517

Gnomad4 SAS

AF:

0.00807

Gnomad4 FIN

AF:

0.0297

Gnomad4 NFE

AF:

0.00788

Gnomad4 OTH

AF:

0.0151

Alfa

AF:

0.00835

Hom.:

Bravo

AF:

0.0198

Asia WGS

AF:

0.0380

AC:

131

AN:

3478

EpiCase

AF:

0.00731

EpiControl

AF:

0.00616

ClinVar

Significance: Benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 20, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

not specified

Benign:3

Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	May 27, 2015	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

COFS syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Cockayne syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Macular degeneration

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

6.0

DANN

Benign

0.76

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