rs1018603

Positions:

• chr10-49520325-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000124.4(ERCC6):​c.1397+3708G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 152,088 control chromosomes in the GnomAD database, including 55,040 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.85 (55040 hom., cov: 31)
• Consequence: ERCC6 NM_000124.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

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]

PGBD3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERCC6	NM_000124.4	c.1397+3708G>T		intron_variant		ENST00000355832.10
ERCC6	NM_001277058.2	c.1398-3204G>T		intron_variant		ENST00000447839.7
PGBD3	NM_170753.3	c.-7-3204G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERCC6	ENST00000355832.10	c.1397+3708G>T		intron_variant		1	NM_000124.4	P1
ERCC6	ENST00000447839.7	c.1398-3204G>T		intron_variant		2	NM_001277058.2

Frequencies

GnomAD3 genomes AF: 0.847 AC: 128757 AN: 151968 Hom.: 55022 Cov.: 31

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.901

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.868

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.847 AC: 128823 AN: 152088 Hom.: 55040 Cov.: 31 AF XY: 0.853 AC XY: 63404 AN XY: 74364

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.909

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.944

Gnomad4 FIN AF: 0.899

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.870

Alfa AF: 0.879 Hom.: 96617

Bravo AF: 0.841

Asia WGS AF: 0.958 AC: 3332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.057
DANN	Benign	0.62

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

Other links and lift over

dbSNP: rs1018603; hg19: chr10-50728371;