Variant 5-111729731-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_004772.4(NREP):c.*1190A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,520 control chromosomes in the GnomAD database, including 11,844 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.34 ( 11838 hom., cov: 33)

Exomes 𝑓: 0.18 ( 6 hom. )

Consequence

NREP
NM_004772.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.44

Variant links:

Genes affected

NREP (HGNC:16834): (neuronal regeneration related protein) Predicted to be involved in axon regeneration; regulation of neuron differentiation; and regulation of transforming growth factor beta receptor signaling pathway. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

NREP links:

STARD4-AS1 (HGNC:):

STARD4-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.24).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NREP	NM_004772.4 linkuse as main transcript	c.*1190A>C		3_prime_UTR_variant	4/4	ENST00000257435.12	NP_004763.1	Q16612-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NREP	ENST00000257435.12 linkuse as main transcript	c.*1190A>C		3_prime_UTR_variant	4/4	1	NM_004772.4	ENSP00000257435.7		Q16612-1

Frequencies

GnomAD3 genomes

AF:

0.344

AC:

52294

AN:

151974

Hom.:

11809

Cov.:

show subpopulations

Gnomad AFR

AF:

0.649

Gnomad AMI

AF:

0.162

Gnomad AMR

AF:

0.311

Gnomad ASJ

AF:

0.191

Gnomad EAS

AF:

0.330

Gnomad SAS

AF:

0.165

Gnomad FIN

AF:

0.177

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.217

Gnomad OTH

AF:

0.323

GnomAD4 exome

AF:

0.180

AC:

AN:

428

Hom.:

Cov.:

AF XY:

0.202

AC XY:

AN XY:

258

show subpopulations

Gnomad4 FIN exome

AF:

0.175

Gnomad4 NFE exome

AF:

0.500

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.344

AC:

52364

AN:

152092

Hom.:

11838

Cov.:

AF XY:

0.339

AC XY:

25214

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.650

Gnomad4 AMR

AF:

0.310

Gnomad4 ASJ

AF:

0.191

Gnomad4 EAS

AF:

0.330

Gnomad4 SAS

AF:

0.164

Gnomad4 FIN

AF:

0.177

Gnomad4 NFE

AF:

0.217

Gnomad4 OTH

AF:

0.322

Alfa

AF:

0.109

Hom.:

159

Bravo

AF:

0.371

Asia WGS

AF:

0.265

AC:

923

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.24

CADD

Benign

DANN

Benign

0.91

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.

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