rs2240320
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006836.2(GCN1):c.2750-300T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 151,404 control chromosomes in the GnomAD database, including 6,321 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 0.25 ( 6321 hom., cov: 30)
Consequence
GCN1
NM_006836.2 intron
NM_006836.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.88
Genes affected
GCN1 (HGNC:4199): (GCN1 activator of EIF2AK4) Enables RNA binding activity and cadherin binding activity. Predicted to be involved in cellular response to leucine starvation and positive regulation of transcription from RNA polymerase II promoter in response to stress. Located in cytosol. [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=-1.05).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GCN1 | NM_006836.2 | c.2750-300T>C | intron_variant | ENST00000300648.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GCN1 | ENST00000300648.7 | c.2750-300T>C | intron_variant | 1 | NM_006836.2 | P1 | |||
GCN1 | ENST00000547369.5 | n.362-300T>C | intron_variant, non_coding_transcript_variant | 3 | |||||
GCN1 | ENST00000550471.1 | n.763-300T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.251 AC: 37945AN: 151286Hom.: 6291 Cov.: 30
GnomAD3 genomes
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37945
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30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.251 AC: 38014AN: 151404Hom.: 6321 Cov.: 30 AF XY: 0.252 AC XY: 18624AN XY: 73970
GnomAD4 genome
?
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AC:
38014
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151404
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30
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18624
AN XY:
73970
Gnomad4 AFR
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1225
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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