Variant chr8-11785950-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_145043.4(NEIL2):c.689-13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 1,610,756 control chromosomes in the GnomAD database, including 44,963 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 0.25 ( 4936 hom., cov: 32)

Exomes 𝑓: 0.23 ( 40027 hom. )

Consequence

NEIL2
NM_145043.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.562

Variant links:

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]

NEIL2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NEIL2	NM_145043.4 link	c.689-13C>T		intron_variant		ENST00000284503.7	NP_659480.1	Q969S2-1A0A024R361

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NEIL2	ENST00000284503.7 link	c.689-13C>T		intron_variant		2	NM_145043.4	ENSP00000284503.6		Q969S2-1

Frequencies

GnomAD3 genomes

AF:

0.251

AC:

38105

AN:

151918

Hom.:

4930

Cov.:

show subpopulations

Gnomad AFR

AF:

0.318

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.194

Gnomad ASJ

AF:

0.292

Gnomad EAS

AF:

0.284

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.230

Gnomad OTH

AF:

0.245

GnomAD3 exomes

AF:

0.228

AC:

56910

AN:

249942

Hom.:

6772

AF XY:

0.227

AC XY:

30662

AN XY:

135294

show subpopulations

Gnomad AFR exome

AF:

0.325

Gnomad AMR exome

AF:

0.158

Gnomad ASJ exome

AF:

0.292

Gnomad EAS exome

AF:

0.283

Gnomad SAS exome

AF:

0.186

Gnomad FIN exome

AF:

0.225

Gnomad NFE exome

AF:

0.231

Gnomad OTH exome

AF:

0.247

GnomAD4 exome

AF:

0.231

AC:

337529

AN:

1458720

Hom.:

40027

Cov.:

AF XY:

0.231

AC XY:

167841

AN XY:

725768

show subpopulations

Gnomad4 AFR exome

AF:

0.329

Gnomad4 AMR exome

AF:

0.165

Gnomad4 ASJ exome

AF:

0.288

Gnomad4 EAS exome

AF:

0.265

Gnomad4 SAS exome

AF:

0.189

Gnomad4 FIN exome

AF:

0.227

Gnomad4 NFE exome

AF:

0.231

Gnomad4 OTH exome

AF:

0.244

GnomAD4 genome

AF:

0.251

AC:

38129

AN:

152036

Hom.:

4936

Cov.:

AF XY:

0.248

AC XY:

18413

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.318

Gnomad4 AMR

AF:

0.194

Gnomad4 ASJ

AF:

0.292

Gnomad4 EAS

AF:

0.283

Gnomad4 SAS

AF:

0.176

Gnomad4 FIN

AF:

0.211

Gnomad4 NFE

AF:

0.230

Gnomad4 OTH

AF:

0.242

Alfa

AF:

0.258

Hom.:

1272

Bravo

AF:

0.253

Asia WGS

AF:

0.212

AC:

737

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.3

DANN

Benign

0.59

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over