Genetic Variant NEIL1:c.435-818delT (chr15-75351274-CT-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001352519.2(NEIL1):c.100-8delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.016 ( 8 hom., cov: 0)

Exomes 𝑓: 0.14 ( 0 hom. )

Consequence

NEIL1
NM_001352519.2 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0650

Variant links:

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]

NEIL1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NEIL1	NM_024608.4 link	c.435-818delT		intron_variant	Intron 2 of 9	ENST00000355059.9	NP_078884.2	Q96FI4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NEIL1	ENST00000355059.9 link	c.435-836delT		intron_variant	Intron 2 of 9	2	NM_024608.4	ENSP00000347170.4		Q96FI4

Frequencies

GnomAD3 genomes

AF:

0.0155

AC:

1883

AN:

121112

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00926

Gnomad AMI

AF:

0.0111

Gnomad AMR

AF:

0.0158

Gnomad ASJ

AF:

0.00963

Gnomad EAS

AF:

0.00102

Gnomad SAS

AF:

0.0296

Gnomad FIN

AF:

0.0116

Gnomad MID

AF:

0.0122

Gnomad NFE

AF:

0.0196

Gnomad OTH

AF:

0.0222

GnomAD4 exome

AF:

0.141

AC:

30839

AN:

219222

Hom.:

Cov.:

AF XY:

0.140

AC XY:

17559

AN XY:

125858

show subpopulations

Gnomad4 AFR exome

AF:

0.176

Gnomad4 AMR exome

AF:

0.142

Gnomad4 ASJ exome

AF:

0.131

Gnomad4 EAS exome

AF:

0.125

Gnomad4 SAS exome

AF:

0.124

Gnomad4 FIN exome

AF:

0.133

Gnomad4 NFE exome

AF:

0.146

Gnomad4 OTH exome

AF:

0.148

GnomAD4 genome

AF:

0.0155

AC:

1882

AN:

121106

Hom.:

Cov.:

AF XY:

0.0159

AC XY:

898

AN XY:

56372

show subpopulations

Gnomad4 AFR

AF:

0.00925

Gnomad4 AMR

AF:

0.0159

Gnomad4 ASJ

AF:

0.00963

Gnomad4 EAS

AF:

0.00102

Gnomad4 SAS

AF:

0.0294

Gnomad4 FIN

AF:

0.0116

Gnomad4 NFE

AF:

0.0196

Gnomad4 OTH

AF:

0.0220

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

15-75351274-CTTTTTTTTT-CTTTTTTTT

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