1-71611116-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173808.3(NEGR1):c.698G>T(p.Gly233Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,600 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173808.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEGR1 | NM_173808.3 | c.698G>T | p.Gly233Val | missense_variant | 5/7 | ENST00000357731.10 | |
NEGR1 | XM_011541200.4 | c.698G>T | p.Gly233Val | missense_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEGR1 | ENST00000357731.10 | c.698G>T | p.Gly233Val | missense_variant | 5/7 | 1 | NM_173808.3 | P1 | |
NEGR1 | ENST00000306821.3 | c.314G>T | p.Gly105Val | missense_variant | 5/7 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 151974Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251230Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135870
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461626Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 727138
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 151974Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74222
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2022 | The c.698G>T (p.G233V) alteration is located in exon 5 (coding exon 5) of the NEGR1 gene. This alteration results from a G to T substitution at nucleotide position 698, causing the glycine (G) at amino acid position 233 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at