19-45351413-C-T

Variant names:

• chr19-45351413-C-T
• rs534559459
• NM_000400.4:c.*216G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS1

The NM_000400.4(ERCC2):​c.*216G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000502 in 1,597,522 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0018 (1 hom., cov: 32)
  • Exomes 𝑓: 0.00036 (1 hom.)
• Consequence: ERCC2 NM_000400.4 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.867

Genes affected

ERCC2 (HGNC:3434): (ERCC excision repair 2, TFIIH core complex helicase subunit) The nucleotide excision repair pathway is a mechanism to repair damage to DNA. The protein encoded by this gene is involved in transcription-coupled nucleotide excision repair and is an integral member of the basal transcription factor BTF2/TFIIH complex. The gene product has ATP-dependent DNA helicase activity and belongs to the RAD3/XPD subfamily of helicases. Defects in this gene can result in three different disorders, the cancer-prone syndrome xeroderma pigmentosum complementation group D, trichothiodystrophy, and Cockayne syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]

KLC3 (HGNC:20717): (kinesin light chain 3) This gene encodes a member of the kinesin light chain gene family. Kinesins are molecular motors involved in the transport of cargo along microtubules, and are composed of two kinesin heavy chain (KHC) and two kinesin light chain (KLC) molecules. KLCs are thought to typically be involved in binding cargo and regulating kinesin activity. In the rat, a protein similar to this gene product is expressed in post-meiotic spermatids, where it associates with structural components of sperm tails and mitochondria. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 19-45351413-C-T is Benign according to our data. Variant chr19-45351413-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 892628.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00181 (275/152306) while in subpopulation AFR AF = 0.00524 (218/41568). AF 95% confidence interval is 0.00467. There are 1 homozygotes in GnomAd4. There are 141 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position FAILED quality control check.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERCC2	NM_000400.4	c.*216G>A		3_prime_UTR_variant	Exon 23 of 23	ENST00000391945.10	NP_000391.1
KLC3	NM_177417.3	c.*56C>T		3_prime_UTR_variant	Exon 13 of 13	ENST00000391946.7	NP_803136.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ERCC2	ENST00000391945	c.*216G>A		3_prime_UTR_variant	Exon 23 of 23	1	NM_000400.4	ENSP00000375809.4
KLC3	ENST00000391946.7	c.*56C>T		3_prime_UTR_variant	Exon 13 of 13	1	NM_177417.3	ENSP00000375810.2

Frequencies

GnomAD3 genomes AF: 0.00179 AC: 272 AN: 152188 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.00519

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00190

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000147

Gnomad OTH AF: 0.00239

GnomAD4 exome AF: 0.000365 AC: 527 AN: 1445216 Hom.: 1 Cov.: 37 AF XY: 0.000366 AC XY: 263 AN XY: 718214

Gnomad4 AFR exome AF: 0.00579 AC: 193 AN: 33324

Gnomad4 AMR exome AF: 0.000834 AC: 37 AN: 44368

Gnomad4 ASJ exome AF: 0.00351 AC: 91 AN: 25938

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 39524

Gnomad4 SAS exome AF: 0.0000116 AC: 1 AN: 85908

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 43326

Gnomad4 NFE exome AF: 0.000134 AC: 148 AN: 1107210

Gnomad4 Remaining exome AF: 0.000885 AC: 53 AN: 59890

GnomAD4 genome AF: 0.00181 AC: 275 AN: 152306 Hom.: 1 Cov.: 32 AF XY: 0.00189 AC XY: 141 AN XY: 74492

Gnomad4 AFR AF: 0.00524 AC: 0.00524442 AN: 0.00524442

Gnomad4 AMR AF: 0.00190 AC: 0.00189815 AN: 0.00189815

Gnomad4 ASJ AF: 0.00374 AC: 0.00374424 AN: 0.00374424

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.00 AC: 0 AN: 0

Gnomad4 FIN AF: 0.00 AC: 0 AN: 0

Gnomad4 NFE AF: 0.000147 AC: 0.000147003 AN: 0.000147003

Gnomad4 OTH AF: 0.00236 AC: 0.00236295 AN: 0.00236295

Alfa AF: 0.000318 Hom.: 0

Bravo AF: 0.00194

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Xeroderma pigmentosum, group D Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.46
DANN	Benign	0.74
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: rs534559459; hg19: chr19-45854671;