Genetic Variant NEIL1:c.435-822_435-818dupTTTTT (chr15-75351274-C-CTTTTT) – 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.100-12_100-8dupTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0044 ( 13 hom., cov: 0)

Exomes 𝑓: 0.0031 ( 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

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NEIL1	NM_024608.4 link	c.435-822_435-818dupTTTTT		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_435-836insTTTTT		intron_variant	Intron 2 of 9	2	NM_024608.4	ENSP00000347170.4		Q96FI4

Frequencies

GnomAD3 genomes

AF:

0.00443

AC:

536

AN:

121102

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000511

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0122

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0757

Gnomad SAS

AF:

0.00194

Gnomad FIN

AF:

0.00801

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000642

Gnomad OTH

AF:

0.00617

GnomAD4 exome

AF:

0.00313

AC:

752

AN:

240284

Hom.:

Cov.:

AF XY:

0.00289

AC XY:

400

AN XY:

138328

show subpopulations

Gnomad4 AFR exome

AF:

0.000358

Gnomad4 AMR exome

AF:

0.0111

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0377

Gnomad4 SAS exome

AF:

0.00168

Gnomad4 FIN exome

AF:

0.00953

Gnomad4 NFE exome

AF:

0.000432

Gnomad4 OTH exome

AF:

0.00303

GnomAD4 genome

AF:

0.00443

AC:

536

AN:

121096

Hom.:

Cov.:

AF XY:

0.00483

AC XY:

272

AN XY:

56356

show subpopulations

Gnomad4 AFR

AF:

0.000511

Gnomad4 AMR

AF:

0.0122

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0757

Gnomad4 SAS

AF:

0.00194

Gnomad4 FIN

AF:

0.00801

Gnomad4 NFE

AF:

0.000642

Gnomad4 OTH

AF:

0.00611

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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-CTTTTTTTTTTTTTT

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