Genetic Variant NEIL1:c.435-818dupT (chr15-75351274-C-CT) – 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.100-8dupT 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 0.40 ( 10950 hom., cov: 0)

Exomes 𝑓: 0.22 ( 28 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

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NEIL1	NM_024608.4 link	c.435-818dupT		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.435-837_435-836insT		intron_variant	Intron 2 of 9	2	NM_024608.4	ENSP00000347170.4		Q96FI4

Frequencies

GnomAD3 genomes

AF:

0.397

AC:

48086

AN:

121070

Hom.:

10964

Cov.:

show subpopulations

Gnomad AFR

AF:

0.241

Gnomad AMI

AF:

0.383

Gnomad AMR

AF:

0.415

Gnomad ASJ

AF:

0.447

Gnomad EAS

AF:

0.491

Gnomad SAS

AF:

0.542

Gnomad FIN

AF:

0.345

Gnomad MID

AF:

0.350

Gnomad NFE

AF:

0.468

Gnomad OTH

AF:

0.380

GnomAD4 exome

AF:

0.219

AC:

49556

AN:

225920

Hom.:

Cov.:

AF XY:

0.219

AC XY:

28553

AN XY:

130164

show subpopulations

Gnomad4 AFR exome

AF:

0.131

Gnomad4 AMR exome

AF:

0.233

Gnomad4 ASJ exome

AF:

0.173

Gnomad4 EAS exome

AF:

0.227

Gnomad4 SAS exome

AF:

0.243

Gnomad4 FIN exome

AF:

0.217

Gnomad4 NFE exome

AF:

0.216

Gnomad4 OTH exome

AF:

0.217

GnomAD4 genome

AF:

0.397

AC:

48058

AN:

121064

Hom.:

10950

Cov.:

AF XY:

0.390

AC XY:

21953

AN XY:

56336

show subpopulations

Gnomad4 AFR

AF:

0.241

Gnomad4 AMR

AF:

0.415

Gnomad4 ASJ

AF:

0.447

Gnomad4 EAS

AF:

0.490

Gnomad4 SAS

AF:

0.541

Gnomad4 FIN

AF:

0.345

Gnomad4 NFE

AF:

0.468

Gnomad4 OTH

AF:

0.378

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)

0.0

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.

15-75351274-CTTTTTTTTT-CTTTTTTTTTT

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