rs2821238
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173808.3(NEGR1):c.176+156899G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.942 in 152,066 control chromosomes in the GnomAD database, including 67,695 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 0.94 ( 67695 hom., cov: 32)
Consequence
NEGR1
NM_173808.3 intron
NM_173808.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0670
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEGR1 | NM_173808.3 | c.176+156899G>T | intron_variant | ENST00000357731.10 | |||
NEGR1 | XM_011541200.4 | c.176+156899G>T | intron_variant | ||||
NEGR1 | XM_011541201.4 | c.176+156899G>T | intron_variant | ||||
NEGR1 | XM_017000961.3 | c.176+156899G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEGR1 | ENST00000357731.10 | c.176+156899G>T | intron_variant | 1 | NM_173808.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.942 AC: 143084AN: 151948Hom.: 67652 Cov.: 32
GnomAD3 genomes
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151948
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.942 AC: 143184AN: 152066Hom.: 67695 Cov.: 32 AF XY: 0.944 AC XY: 70210AN XY: 74344
GnomAD4 genome
?
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143184
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152066
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32
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70210
AN XY:
74344
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3408
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3442
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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