chr5-111975314-T-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NR_046678.1(NREP-AS1):n.443+808T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000035 in 1,399,324 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000035 ( 0 hom. )
Consequence
NREP-AS1
NR_046678.1 intron, non_coding_transcript
NR_046678.1 intron, non_coding_transcript
Scores
1
1
13
Clinical Significance
Conservation
PhyloP100: -0.581
Genes affected
NREP-AS1 (HGNC:40780): (NREP antisense RNA 1)
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.073062986).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NREP-AS1 | NR_046678.1 | n.443+808T>A | intron_variant, non_coding_transcript_variant | ||||
NREP | NM_001142475.2 | c.95A>T | p.Lys32Ile | missense_variant | 2/4 | ||
NREP | NM_001142474.2 | c.95A>T | p.Lys32Ile | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NREP-AS1 | ENST00000507222.5 | n.443+808T>A | intron_variant, non_coding_transcript_variant | 3 | |||||
NREP | ENST00000395634.7 | c.95A>T | p.Lys32Ile | missense_variant | 2/4 | 2 | |||
NREP | ENST00000450761.6 | c.-59+22010A>T | intron_variant | 4 | P1 | ||||
NREP-AS1 | ENST00000503242.1 | n.241+808T>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.0000260 AC: 4AN: 154020Hom.: 0 AF XY: 0.0000367 AC XY: 3AN XY: 81720
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GnomAD4 exome AF: 0.0000350 AC: 49AN: 1399324Hom.: 0 Cov.: 30 AF XY: 0.0000449 AC XY: 31AN XY: 690170
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GnomAD4 genome Cov.: 32
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32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 27, 2023 | The c.95A>T (p.K32I) alteration is located in exon 2 (coding exon 2) of the NREP gene. This alteration results from a A to T substitution at nucleotide position 95, causing the lysine (K) at amino acid position 32 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at