2-127257353-A-AT

Variant names:

• chr2-127257353-A-AT
• rs576058879
• ENST00000285398:c.*242dupA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_000122.2(ERCC3):​c.*242dupA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00259 in 556,846 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★★).

• Frequency:
  • Genomes: 𝑓 0.0023 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0027 (1 hom.)
• Consequence: ERCC3 NM_000122.2 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:2
• Conservation: PhyloP100: -1.40

Genes affected

ERCC3 (HGNC:3435): (ERCC excision repair 3, TFIIH core complex helicase subunit) This gene encodes an ATP-dependent DNA helicase that functions in nucleotide excision repair. The encoded protein is a subunit of basal transcription factor 2 (TFIIH) and, therefore, also functions in class II transcription. Mutations in this gene are associated with Xeroderma pigmentosum B, Cockayne's syndrome, and trichothiodystrophy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERCC3	NM_000122.2	c.*242dupA		3_prime_UTR_variant	Exon 15 of 15	ENST00000285398.7	NP_000113.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ERCC3	ENST00000285398	c.*242dupA		3_prime_UTR_variant	Exon 15 of 15	1	NM_000122.2	ENSP00000285398.2

Frequencies

GnomAD3 genomes AF: 0.00231 AC: 352 AN: 152140 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000820

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00164

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00407

Gnomad OTH AF: 0.00431

GnomAD4 exome AF: 0.00269 AC: 1090 AN: 404588 Hom.: 1 Cov.: 3 AF XY: 0.00247 AC XY: 528 AN XY: 213778

Gnomad4 AFR exome AF: 0.000346 AC: 4 AN: 11552

Gnomad4 AMR exome AF: 0.000882 AC: 15 AN: 17000

Gnomad4 ASJ exome AF: 0.000817 AC: 10 AN: 12242

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 26452

Gnomad4 SAS exome AF: 0.000135 AC: 6 AN: 44512

Gnomad4 FIN exome AF: 0.000348 AC: 12 AN: 34464

Gnomad4 NFE exome AF: 0.00418 AC: 977 AN: 233912

Gnomad4 Remaining exome AF: 0.00289 AC: 66 AN: 22804

GnomAD4 genome AF: 0.00231 AC: 352 AN: 152258 Hom.: 0 Cov.: 32 AF XY: 0.00203 AC XY: 151 AN XY: 74454

Gnomad4 AFR AF: 0.000818 AC: 0.000817976 AN: 0.000817976

Gnomad4 AMR AF: 0.00164 AC: 0.00163613 AN: 0.00163613

Gnomad4 ASJ AF: 0.000576 AC: 0.000576037 AN: 0.000576037

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.000622 AC: 0.000621891 AN: 0.000621891

Gnomad4 FIN AF: 0.000189 AC: 0.00018875 AN: 0.00018875

Gnomad4 NFE AF: 0.00407 AC: 0.00407221 AN: 0.00407221

Gnomad4 OTH AF: 0.00426 AC: 0.00426136 AN: 0.00426136

Alfa AF: 0.00243 Hom.: 0

Bravo AF: 0.00250

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Xeroderma pigmentosum Uncertain:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Uncertain:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mutation Taster		=100/0	polymorphism

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: rs576058879; hg19: chr2-128014929;