NM_145043.4:c.*190T>C

Variant names:

• chr8-11786463-T-C
• rs6997097
• NM_145043.4:c.*190T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145043.4(NEIL2):​c.*190T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0619 in 626,096 control chromosomes in the GnomAD database, including 1,518 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 0.051 (265 hom., cov: 31)
  • Exomes 𝑓: 0.065 (1253 hom.)
• Consequence: NEIL2 NM_145043.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93
• Publications: 7 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0903 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145043.4. 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.*190T>C		3_prime_UTR	Exon 5 of 5	NP_659480.1
	NEIL2	NR_146180.2		n.1845T>C		non_coding_transcript_exon	Exon 5 of 5
	NEIL2	NR_146181.2		n.2012T>C		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEIL2	ENST00000284503.7	TSL:2 MANE Select	c.*190T>C		3_prime_UTR	Exon 5 of 5	ENSP00000284503.6
	NEIL2	ENST00000436750.7	TSL:1	c.*190T>C		3_prime_UTR	Exon 5 of 5	ENSP00000394023.2
	NEIL2	ENST00000524741.1	TSL:2	n.1289T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0508 AC: 7725 AN: 152094 Hom.: 266 Cov.: 31

Gnomad AFR AF: 0.0130

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0386

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.0975

Gnomad FIN AF: 0.0723

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0756

Gnomad OTH AF: 0.0533

GnomAD4 exome AF: 0.0655 AC: 31030 AN: 473886 Hom.: 1253 Cov.: 5 AF XY: 0.0683 AC XY: 17091 AN XY: 250274

African (AFR) AF: 0.0145 AC: 188 AN: 12962

American (AMR) AF: 0.0346 AC: 769 AN: 22252

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 230 AN: 14700

East Asian (EAS) AF: 0.000837 AC: 26 AN: 31058

South Asian (SAS) AF: 0.0991 AC: 4732 AN: 47748

European-Finnish (FIN) AF: 0.0703 AC: 2225 AN: 31644

Middle Eastern (MID) AF: 0.0640 AC: 131 AN: 2046

European-Non Finnish (NFE) AF: 0.0743 AC: 21137 AN: 284600

Other (OTH) AF: 0.0592 AC: 1592 AN: 26876

GnomAD4 genome AF: 0.0507 AC: 7722 AN: 152210 Hom.: 265 Cov.: 31 AF XY: 0.0507 AC XY: 3770 AN XY: 74406

African (AFR) AF: 0.0130 AC: 539 AN: 41542

American (AMR) AF: 0.0385 AC: 589 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3472

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5172

South Asian (SAS) AF: 0.0976 AC: 470 AN: 4814

European-Finnish (FIN) AF: 0.0723 AC: 766 AN: 10598

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0755 AC: 5137 AN: 68008

Other (OTH) AF: 0.0527 AC: 111 AN: 2106

Alfa AF: 0.0606 Hom.: 186

Bravo AF: 0.0461

Asia WGS AF: 0.0350 AC: 124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.1
DANN	Benign	0.66
PhyloP100		1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6997097; hg19: chr8-11643972;