Variant 3-113019471-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_015412.4(NEPRO):c.106+71G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 1,300,084 control chromosomes in the GnomAD database, including 380,416 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.69 ( 37247 hom., cov: 34)

Exomes 𝑓: 0.77 ( 343169 hom. )

Consequence

NEPRO
NM_015412.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.607

Variant links:

Genes affected

NEPRO (HGNC:24496): (nucleolus and neural progenitor protein) Predicted to be involved in negative regulation of neuron differentiation and positive regulation of Notch signaling pathway. Predicted to be located in nucleolus. Predicted to be active in nucleus. Implicated in anauxetic dysplasia 3. [provided by Alliance of Genome Resources, Apr 2022]

NEPRO links:

NEPRO-AS1 (HGNC:41049): (NEPRO antisense RNA 1)

NEPRO-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP6

Variant 3-113019471-C-T is Benign according to our data. Variant chr3-113019471-C-T is described in ClinVar as [Benign]. Clinvar id is 1192596.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NEPRO	NM_015412.4 link	c.106+71G>A		intron_variant		ENST00000314400.10	NP_056227.2	Q6NW34-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NEPRO	ENST00000314400.10 link	c.106+71G>A		intron_variant		1	NM_015412.4	ENSP00000320251.5		Q6NW34-1

Frequencies

GnomAD3 genomes

AF:

0.686

AC:

104345

AN:

152062

Hom.:

37230

Cov.:

show subpopulations

Gnomad AFR

AF:

0.510

Gnomad AMI

AF:

0.777

Gnomad AMR

AF:

0.753

Gnomad ASJ

AF:

0.822

Gnomad EAS

AF:

0.348

Gnomad SAS

AF:

0.712

Gnomad FIN

AF:

0.659

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.798

Gnomad OTH

AF:

0.703

GnomAD4 exome

AF:

0.767

AC:

879922

AN:

1147904

Hom.:

343169

AF XY:

0.766

AC XY:

444316

AN XY:

580106

show subpopulations

Gnomad4 AFR exome

AF:

0.503

Gnomad4 AMR exome

AF:

0.778

Gnomad4 ASJ exome

AF:

0.813

Gnomad4 EAS exome

AF:

0.356

Gnomad4 SAS exome

AF:

0.719

Gnomad4 FIN exome

AF:

0.679

Gnomad4 NFE exome

AF:

0.801

Gnomad4 OTH exome

AF:

0.746

GnomAD4 genome

AF:

0.686

AC:

104389

AN:

152180

Hom.:

37247

Cov.:

AF XY:

0.679

AC XY:

50550

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.510

Gnomad4 AMR

AF:

0.752

Gnomad4 ASJ

AF:

0.822

Gnomad4 EAS

AF:

0.349

Gnomad4 SAS

AF:

0.712

Gnomad4 FIN

AF:

0.659

Gnomad4 NFE

AF:

0.798

Gnomad4 OTH

AF:

0.705

Alfa

AF:

0.737

Hom.:

5262

Bravo

AF:

0.682

Asia WGS

AF:

0.551

AC:

1921

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Anauxetic dysplasia 3

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

DANN

Benign

0.96

RBP_binding_hub_radar

0.77

RBP_regulation_power_radar

1.8

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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