rs10475
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001674.4(ATF3):c.*716T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 153,034 control chromosomes in the GnomAD database, including 43,965 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 0.75 ( 43683 hom., cov: 32)
Exomes 𝑓: 0.79 ( 282 hom. )
Consequence
ATF3
NM_001674.4 3_prime_UTR
NM_001674.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0360
Genes affected
ATF3 (HGNC:785): (activating transcription factor 3) This gene encodes a member of the mammalian activation transcription factor/cAMP responsive element-binding (CREB) protein family of transcription factors. This gene is induced by a variety of signals, including many of those encountered by cancer cells, and is involved in the complex process of cellular stress response. Multiple transcript variants encoding different isoforms have been found for this gene. It is possible that alternative splicing of this gene may be physiologically important in the regulation of target genes. [provided by RefSeq, Apr 2011]
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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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATF3 | ENST00000341491.9 | c.*716T>C | 3_prime_UTR_variant | Exon 4 of 4 | 1 | NM_001674.4 | ENSP00000344352.4 | |||
ATF3 | ENST00000366987.6 | c.*716T>C | 3_prime_UTR_variant | Exon 4 of 4 | 1 | ENSP00000355954.2 | ||||
ATF3 | ENST00000492118.2 | n.1597T>C | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.754 AC: 114606AN: 152026Hom.: 43652 Cov.: 32
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GnomAD4 exome AF: 0.789 AC: 702AN: 890Hom.: 282 Cov.: 0 AF XY: 0.798 AC XY: 404AN XY: 506
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GnomAD4 genome AF: 0.754 AC: 114699AN: 152144Hom.: 43683 Cov.: 32 AF XY: 0.750 AC XY: 55810AN XY: 74402
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at