rs56037884

Variant names:

• chr8-11769688-CCGCATGGGCCGCCGAGC-A
• rs56037884
• ENST00000436750.7:c.-106_-89delCCGCATGGGCCGCCGAGCinsA

Variant summary

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

The ENST00000436750.7(NEIL2):​c.-106_-89delCCGCATGGGCCGCCGAGCinsA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: NEIL2 ENST00000436750.7 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.729
• Publications: 1 publications found

Genes affected

NEIL2 (HGNC:18956): (nei like DNA glycosylase 2) This gene encodes a member of the Fpg/Nei family of DNA glycosylases. These glycosylases initiate the first step in base excision repair by cleaving oxidatively damaged bases and introducing a DNA strand break via their abasic site lyase activity. This enzyme is primarily associated with DNA repair during transcription and acts prefentially on cytosine-derived lesions, particularly 5-hydroxyuracil and 5-hydroxycytosine. It contains an N-terminal catalytic domain, a hinge region, and a C-terminal DNA-binding domain with helix-two-turn-helix and zinc finger motifs. This enzyme interacts with the X-ray cross complementing factor 1 scaffold protein as part of a multi-protein DNA repair complex. A pseudogene of this gene has been identified. [provided by RefSeq, Mar 2017]

LOC124901888 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436750.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEIL2	NM_145043.4	MANE Select	c.-650_-633delCCGCATGGGCCGCCGAGCinsA		upstream_gene	N/A	NP_659480.1
	NEIL2	NM_001135746.3		c.-106_-89delCCGCATGGGCCGCCGAGCinsA		upstream_gene	N/A	NP_001129218.1
	NEIL2	NM_001349442.2		c.-268_-251delCCGCATGGGCCGCCGAGCinsA		upstream_gene	N/A	NP_001336371.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEIL2	ENST00000436750.7	TSL:1	c.-106_-89delCCGCATGGGCCGCCGAGCinsA		5_prime_UTR	Exon 1 of 5	ENSP00000394023.2
	NEIL2	ENST00000455213.6	TSL:5	c.-268_-251delCCGCATGGGCCGCCGAGCinsA		5_prime_UTR	Exon 1 of 6	ENSP00000397538.2
	NEIL2	ENST00000455213.6	TSL:5	c.-268_-251delCCGCATGGGCCGCCGAGCinsA		non_coding_transcript	N/A	ENSP00000397538.2

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs56037884; hg19: chr8-11627197;