Variant rs5745925 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_024608.4(NEIL1):c.719-114_719-113del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0682 in 1,130,302 control chromosomes in the GnomAD database, including 3,069 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.057 ( 315 hom., cov: 32)

Exomes 𝑓: 0.070 ( 2754 hom. )

Consequence

NEIL1
NM_024608.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.98

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:

MIR631 (HGNC:32887): (microRNA 631) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR631 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 15-75353624-CCT-C is Benign according to our data. Variant chr15-75353624-CCT-C is described in ClinVar as [Benign]. Clinvar id is 1281887.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NEIL1	NM_024608.4 linkuse as main transcript	c.719-114_719-113del		intron_variant		ENST00000355059.9	NP_078884.2
MIR631	NR_030360.1 linkuse as main transcript	n.60_61del		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NEIL1	ENST00000355059.9 linkuse as main transcript	c.719-114_719-113del		intron_variant		2	NM_024608.4	ENSP00000347170	P1
MIR631	ENST00000384904.1 linkuse as main transcript	n.60_61del		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.0569

AC:

8651

AN:

152074

Hom.:

314

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0240

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.0464

Gnomad ASJ

AF:

0.0775

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0230

Gnomad FIN

AF:

0.0859

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0800

Gnomad OTH

AF:

0.0498

GnomAD3 exomes

AF:

0.0589

AC:

14791

AN:

251262

Hom.:

575

AF XY:

0.0593

AC XY:

8057

AN XY:

135870

show subpopulations

Gnomad AFR exome

AF:

0.0225

Gnomad AMR exome

AF:

0.0343

Gnomad ASJ exome

AF:

0.0766

Gnomad EAS exome

AF:

0.000272

Gnomad SAS exome

AF:

0.0295

Gnomad FIN exome

AF:

0.0872

Gnomad NFE exome

AF:

0.0816

Gnomad OTH exome

AF:

0.0656

GnomAD4 exome

AF:

0.0700

AC:

68487

AN:

978110

Hom.:

2754

AF XY:

0.0693

AC XY:

35121

AN XY:

506834

show subpopulations

Gnomad4 AFR exome

AF:

0.0221

Gnomad4 AMR exome

AF:

0.0356

Gnomad4 ASJ exome

AF:

0.0803

Gnomad4 EAS exome

AF:

0.000164

Gnomad4 SAS exome

AF:

0.0311

Gnomad4 FIN exome

AF:

0.0883

Gnomad4 NFE exome

AF:

0.0811

Gnomad4 OTH exome

AF:

0.0611

GnomAD4 genome

AF:

0.0568

AC:

8651

AN:

152192

Hom.:

315

Cov.:

AF XY:

0.0551

AC XY:

4099

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.0239

Gnomad4 AMR

AF:

0.0463

Gnomad4 ASJ

AF:

0.0775

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0230

Gnomad4 FIN

AF:

0.0859

Gnomad4 NFE

AF:

0.0800

Gnomad4 OTH

AF:

0.0488

Alfa

AF:

0.0710

Hom.:

Bravo

AF:

0.0527

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 20, 2019

- -

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over