rs11422837
Your query was ambiguous. Multiple possible variants found:
- chr15-75351274-CTTTTTTTTT-C
- chr15-75351274-CTTTTTTTTT-CT
- chr15-75351274-CTTTTTTTTT-CTT
- chr15-75351274-CTTTTTTTTT-CTTT
- chr15-75351274-CTTTTTTTTT-CTTTT
- chr15-75351274-CTTTTTTTTT-CTTTTT
- chr15-75351274-CTTTTTTTTT-CTTTTTT
- chr15-75351274-CTTTTTTTTT-CTTTTTTT
- chr15-75351274-CTTTTTTTTT-CTTTTTTTT
- chr15-75351274-CTTTTTTTTT-CTTTTTTTTTT
- chr15-75351274-CTTTTTTTTT-CTTTTTTTTTTT
- chr15-75351274-CTTTTTTTTT-CTTTTTTTTTTTT
- chr15-75351274-CTTTTTTTTT-CTTTTTTTTTTTTT
- chr15-75351274-CTTTTTTTTT-CTTTTTTTTTTTTTT
- chr15-75351274-CTTTTTTTTT-CTTTTTTTTTTTTTTT
- chr15-75351274-CTTTTTTTTT-CTTTTTTTTTTTTTTTT
- chr15-75351274-CTTTTTTTTT-CTTTTTTTTTTTTTTTTT
- chr15-75351274-CTTTTTTTTT-CTTTTTTTTTTTTTTTTTT
- chr15-75351274-CTTTTTTTTT-CTTTTTTTTTTTTTTTTTTTTT
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001352519.2(NEIL1):c.100-16_100-8delTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000553 in 361,730 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000083 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000042 ( 0 hom. )
Consequence
NEIL1
NM_001352519.2 splice_region, intron
NM_001352519.2 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.07
Publications
0 publications found
Genes affected
NEIL1 (HGNC:18448): (nei like DNA glycosylase 1) This gene is a member of the Nei endonuclease VIII-like gene family which encodes DNA glycosylases. The encoded enzyme participates in the DNA repair pathway by initiating base excision repair by removing damaged bases, primarily oxidized pyrimidines. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001352519.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NEIL1 | MANE Select | c.435-826_435-818delTTTTTTTTT | intron | N/A | NP_078884.2 | Q96FI4 | |||
| NEIL1 | c.693-826_693-818delTTTTTTTTT | intron | N/A | NP_001243481.1 | Q96FI4 | ||||
| NEIL1 | c.129-826_129-818delTTTTTTTTT | intron | N/A | NP_001339449.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NEIL1 | TSL:2 MANE Select | c.435-836_435-828delTTTTTTTTT | intron | N/A | ENSP00000347170.4 | Q96FI4 | |||
| NEIL1 | TSL:1 | c.435-836_435-828delTTTTTTTTT | intron | N/A | ENSP00000455730.1 | Q96FI4 | |||
| NEIL1 | c.435-836_435-828delTTTTTTTTT | intron | N/A | ENSP00000536974.1 |
Frequencies
GnomAD3 genomes 0.00000825 AC: 1AN: 121146Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
121146
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000416 AC: 1AN: 240584Hom.: 0 AF XY: 0.00000722 AC XY: 1AN XY: 138472 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
240584
Hom.:
AF XY:
AC XY:
1
AN XY:
138472
show subpopulations
African (AFR)
AF:
AC:
0
AN:
5582
American (AMR)
AF:
AC:
0
AN:
16540
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
7802
East Asian (EAS)
AF:
AC:
1
AN:
8230
South Asian (SAS)
AF:
AC:
0
AN:
46392
European-Finnish (FIN)
AF:
AC:
0
AN:
9586
Middle Eastern (MID)
AF:
AC:
0
AN:
846
European-Non Finnish (NFE)
AF:
AC:
0
AN:
134384
Other (OTH)
AF:
AC:
0
AN:
11222
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<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 0.00000825 AC: 1AN: 121146Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 56372 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
121146
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
56372
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33262
American (AMR)
AF:
AC:
1
AN:
11188
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3114
East Asian (EAS)
AF:
AC:
0
AN:
3918
South Asian (SAS)
AF:
AC:
0
AN:
3614
European-Finnish (FIN)
AF:
AC:
0
AN:
4128
Middle Eastern (MID)
AF:
AC:
0
AN:
246
European-Non Finnish (NFE)
AF:
AC:
0
AN:
59240
Other (OTH)
AF:
AC:
0
AN:
1622
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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