NM_005171.5:c.687A>G
Variant names:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_005171.5(ATF1):āc.687A>Gā(p.Glu229Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 1,612,082 control chromosomes in the GnomAD database, including 6,390 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: š 0.063 ( 437 hom., cov: 32)
Exomes š: 0.086 ( 5953 hom. )
Consequence
ATF1
NM_005171.5 synonymous
NM_005171.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.647
Genes affected
ATF1 (HGNC:783): (activating transcription factor 1) This gene encodes an activating transcription factor, which belongs to the ATF subfamily and bZIP (basic-region leucine zipper) family. It influences cellular physiologic processes by regulating the expression of downstream target genes, which are related to growth, survival, and other cellular activities. This protein is phosphorylated at serine 63 in its kinase-inducible domain by serine/threonine kinases, cAMP-dependent protein kinase A, calmodulin-dependent protein kinase I/II, mitogen- and stress-activated protein kinase and cyclin-dependent kinase 3 (cdk-3). Its phosphorylation enhances its transactivation and transcriptional activities, and enhances cell transformation. Fusion of this gene and FUS on chromosome 16 or EWSR1 on chromosome 22 induced by translocation generates chimeric proteins in angiomatoid fibrous histiocytoma and clear cell sarcoma. This gene has a pseudogene on chromosome 6. [provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP7
Synonymous conserved (PhyloP=0.647 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0981 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATF1 | ENST00000262053.8 | c.687A>G | p.Glu229Glu | synonymous_variant | Exon 7 of 7 | 1 | NM_005171.5 | ENSP00000262053.3 | ||
ATF1 | ENST00000551831.5 | n.*284A>G | non_coding_transcript_exon_variant | Exon 6 of 6 | 2 | ENSP00000448987.1 | ||||
ATF1 | ENST00000551831.5 | n.*284A>G | 3_prime_UTR_variant | Exon 6 of 6 | 2 | ENSP00000448987.1 |
Frequencies
GnomAD3 genomes AF: 0.0634 AC: 9649AN: 152156Hom.: 437 Cov.: 32
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GnomAD3 exomes AF: 0.0672 AC: 16744AN: 249302Hom.: 710 AF XY: 0.0693 AC XY: 9330AN XY: 134678
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GnomAD4 exome AF: 0.0859 AC: 125367AN: 1459808Hom.: 5953 Cov.: 31 AF XY: 0.0856 AC XY: 62157AN XY: 726014
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GnomAD4 genome AF: 0.0633 AC: 9646AN: 152274Hom.: 437 Cov.: 32 AF XY: 0.0600 AC XY: 4470AN XY: 74450
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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