X-47638907-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001114123.3(ELK1):c.642C>T(p.Gly214=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000932 in 1,202,108 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 58 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., 8 hem., cov: 23)
Exomes 𝑓: 0.000088 ( 0 hom. 50 hem. )
Consequence
ELK1
NM_001114123.3 synonymous
NM_001114123.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.51
Genes affected
ELK1 (HGNC:3321): (ETS transcription factor ELK1) This gene is a member of the Ets family of transcription factors and of the ternary complex factor (TCF) subfamily. Proteins of the TCF subfamily form a ternary complex by binding to the the serum response factor and the serum response element in the promoter of the c-fos proto-oncogene. The protein encoded by this gene is a nuclear target for the ras-raf-MAPK signaling cascade. This gene produces multiple isoforms by using alternative translational start codons and by alternative splicing. Related pseudogenes have been identified on chromosomes 7 and 14. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
Variant X-47638907-G-A is Benign according to our data. Variant chrX-47638907-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2660434.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-47638907-G-A is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=1.51 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 8 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELK1 | NM_001114123.3 | c.642C>T | p.Gly214= | synonymous_variant | 4/7 | ENST00000376983.8 | |
ELK1 | NM_005229.4 | c.642C>T | p.Gly214= | synonymous_variant | 3/6 | ||
ELK1 | NM_001257168.1 | c.270+372C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELK1 | ENST00000376983.8 | c.642C>T | p.Gly214= | synonymous_variant | 4/7 | 1 | NM_001114123.3 | P1 | |
ELK1 | ENST00000247161.7 | c.642C>T | p.Gly214= | synonymous_variant | 3/6 | 1 | P1 | ||
ELK1 | ENST00000343894.8 | c.270+372C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 17AN: 112578Hom.: 0 Cov.: 23 AF XY: 0.000259 AC XY: 9AN XY: 34722
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GnomAD3 exomes AF: 0.000115 AC: 18AN: 157091Hom.: 0 AF XY: 0.000160 AC XY: 8AN XY: 50037
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GnomAD4 exome AF: 0.0000881 AC: 96AN: 1089476Hom.: 0 Cov.: 33 AF XY: 0.000140 AC XY: 50AN XY: 357156
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GnomAD4 genome AF: 0.000142 AC: 16AN: 112632Hom.: 0 Cov.: 23 AF XY: 0.000230 AC XY: 8AN XY: 34786
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | ELK1: BP4, BP7, BS2 - |
Computational 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
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