chr1-72282401-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_173808.3(NEGR1):c.94C>G(p.Leu32Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00792 in 1,613,908 control chromosomes in the GnomAD database, including 75 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0060 ( 5 hom., cov: 30)
Exomes 𝑓: 0.0081 ( 70 hom. )
Consequence
NEGR1
NM_173808.3 missense
NM_173808.3 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 3.57
Genes affected
NEGR1 (HGNC:17302): (neuronal growth regulator 1) Predicted to act upstream of or within several processes, including feeding behavior; locomotory behavior; and positive regulation of neuron projection development. Predicted to be located in extracellular region and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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 (MetaRNN=0.0052229166).
BP6
?
Variant 1-72282401-G-C is Benign according to our data. Variant chr1-72282401-G-C is described in ClinVar as [Benign]. Clinvar id is 713750.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 5 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEGR1 | NM_173808.3 | c.94C>G | p.Leu32Val | missense_variant | 1/7 | ENST00000357731.10 | |
NEGR1 | XM_011541200.4 | c.94C>G | p.Leu32Val | missense_variant | 1/7 | ||
NEGR1 | XM_011541201.4 | c.94C>G | p.Leu32Val | missense_variant | 1/5 | ||
NEGR1 | XM_017000961.3 | c.94C>G | p.Leu32Val | missense_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEGR1 | ENST00000357731.10 | c.94C>G | p.Leu32Val | missense_variant | 1/7 | 1 | NM_173808.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00602 AC: 914AN: 151920Hom.: 5 Cov.: 30
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GnomAD3 exomes AF: 0.00636 AC: 1599AN: 251382Hom.: 9 AF XY: 0.00647 AC XY: 879AN XY: 135872
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GnomAD4 exome AF: 0.00812 AC: 11874AN: 1461870Hom.: 70 Cov.: 31 AF XY: 0.00780 AC XY: 5673AN XY: 727242
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GnomAD4 genome ? AF: 0.00601 AC: 913AN: 152038Hom.: 5 Cov.: 30 AF XY: 0.00580 AC XY: 431AN XY: 74324
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73
ExAC
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845
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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 | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
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