chr8-25419460-C-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP3BP6_ModerateBS1BS2
The NM_001083111.2(GNRH1):āc.238G>Cā(p.Glu80Gln) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00107 in 1,415,232 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_001083111.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNRH1 | NM_001083111.2 | c.238G>C | p.Glu80Gln | missense_variant, splice_region_variant | 4/4 | ENST00000421054.7 | |
GNRH1 | NM_000825.3 | c.250G>C | p.Glu84Gln | missense_variant, splice_region_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNRH1 | ENST00000421054.7 | c.238G>C | p.Glu80Gln | missense_variant, splice_region_variant | 4/4 | 1 | NM_001083111.2 | P1 | |
GNRH1 | ENST00000276414.4 | c.238G>C | p.Glu80Gln | missense_variant, splice_region_variant | 3/3 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00542 AC: 824AN: 152030Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00141 AC: 351AN: 249030Hom.: 2 AF XY: 0.00104 AC XY: 141AN XY: 135162
GnomAD4 exome AF: 0.000542 AC: 685AN: 1263084Hom.: 5 Cov.: 20 AF XY: 0.000468 AC XY: 299AN XY: 638486
GnomAD4 genome AF: 0.00542 AC: 825AN: 152148Hom.: 6 Cov.: 32 AF XY: 0.00504 AC XY: 375AN XY: 74384
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at