rs10876469
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The 12-53626419-T-G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,466 control chromosomes in the GnomAD database, including 10,111 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 0.36 ( 10084 hom., cov: 32)
Exomes 𝑓: 0.30 ( 27 hom. )
Consequence
ATF7
NM_006856.3 upstream_gene
NM_006856.3 upstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0760
Genes affected
ATF7 (HGNC:792): (activating transcription factor 7) Enables several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; mitogen-activated protein kinase binding activity; and transcription coactivator binding activity. Involved in negative regulation of transcription by RNA polymerase II and positive regulation of transcription by RNA polymerase II. Located in nucleoplasm. Biomarker of colorectal cancer. [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=-0.73).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATF7 | NM_006856.3 | upstream_gene_variant | ENST00000420353.7 | ||||
ATF7-NPFF | NR_159377.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATF7 | ENST00000420353.7 | upstream_gene_variant | 1 | NM_006856.3 | P1 | ||||
ATF7 | ENST00000591397.1 | upstream_gene_variant | 1 | ||||||
ATF7 | ENST00000548446.6 | upstream_gene_variant | 2 | ||||||
ATF7 | ENST00000589726.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.357 AC: 54233AN: 151718Hom.: 10075 Cov.: 32
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GnomAD4 exome AF: 0.305 AC: 192AN: 630Hom.: 27 Cov.: 0 AF XY: 0.320 AC XY: 132AN XY: 412
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GnomAD4 genome ? AF: 0.358 AC: 54283AN: 151836Hom.: 10084 Cov.: 32 AF XY: 0.364 AC XY: 27010AN XY: 74176
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at