Genetic Variant NEIL2:c.*34C>T (chr8-11786307-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_145043.4(NEIL2):c.*34C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000429 in 932,220 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000012 ( 0 hom., cov: 23)

Exomes 𝑓: 0.0000035 ( 0 hom. )

Consequence

NEIL2
NM_145043.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.12

Publications

2 publications found

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 was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NEIL2	NM_145043.4 link	c.*34C>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000284503.7	NP_659480.1	Q969S2-1A0A024R361

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NEIL2	ENST00000284503.7 link	c.*34C>T		3_prime_UTR_variant	Exon 5 of 5	2	NM_145043.4	ENSP00000284503.6		Q969S2-1

Frequencies

GnomAD3 genomes

AF:

0.0000118

AC:

AN:

85022

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000248

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00000929

AC:

AN:

215340

AF XY:

0.0000170

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000213

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000354

AC:

AN:

847198

Hom.:

Cov.:

AF XY:

0.00000475

AC XY:

AN XY:

421332

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

14286

American (AMR)

AF:

0.00

AC:

AN:

29114

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12938

East Asian (EAS)

AF:

0.00

AC:

AN:

19628

South Asian (SAS)

AF:

0.00

AC:

AN:

55648

European-Finnish (FIN)

AF:

0.00

AC:

AN:

30796

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2296

European-Non Finnish (NFE)

AF:

0.00000308

AC:

AN:

648334

Other (OTH)

AF:

0.0000293

AC:

AN:

34158

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000118

AC:

AN:

85022

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

41846

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

18746

American (AMR)

AF:

0.00

AC:

AN:

9808

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1730

East Asian (EAS)

AF:

0.00

AC:

AN:

2700

South Asian (SAS)

AF:

0.00

AC:

AN:

3298

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6602

Middle Eastern (MID)

AF:

0.00

AC:

AN:

132

European-Non Finnish (NFE)

AF:

0.0000248

AC:

AN:

40288

Other (OTH)

AF:

0.00

AC:

AN:

1182

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.47

(source)

DANN

Benign

0.46

PhyloP100

-1.1

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over