chr12-96259757-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_005230.4(ELK3):c.1029G>A(p.Pro343=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0035 in 1,609,998 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0045 ( 5 hom., cov: 33)
Exomes 𝑓: 0.0034 ( 26 hom. )
Consequence
ELK3
NM_005230.4 synonymous
NM_005230.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.181
Genes affected
ELK3 (HGNC:3325): (ETS transcription factor ELK3) This gene encodes a member of the ETS-domain transcription factor family and the ternary complex factor (TCF) subfamily. Proteins in this subfamily regulate transcription when recruited by serum response factor to bind to serum response elements. This protein is activated by signal-induced phosphorylation; studies in rodents suggest that it is a transcriptional inhibitor in the absence of Ras, but activates transcription when Ras is present. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 12-96259757-G-A is Benign according to our data. Variant chr12-96259757-G-A is described in ClinVar as [Benign]. Clinvar id is 779607.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.181 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0034 (4950/1457744) while in subpopulation MID AF= 0.02 (115/5758). AF 95% confidence interval is 0.017. There are 26 homozygotes in gnomad4_exome. There are 2442 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELK3 | NM_005230.4 | c.1029G>A | p.Pro343= | synonymous_variant | 4/5 | ENST00000228741.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELK3 | ENST00000228741.8 | c.1029G>A | p.Pro343= | synonymous_variant | 4/5 | 1 | NM_005230.4 | P1 | |
ELK3 | ENST00000552142.5 | c.234G>A | p.Pro78= | synonymous_variant | 3/4 | 5 | |||
ELK3 | ENST00000549529.1 | n.118G>A | non_coding_transcript_exon_variant | 2/3 | 2 | ||||
ELK3 | ENST00000549985.1 | c.*5G>A | 3_prime_UTR_variant, NMD_transcript_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00448 AC: 681AN: 152136Hom.: 5 Cov.: 33
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GnomAD3 exomes AF: 0.00336 AC: 836AN: 248620Hom.: 3 AF XY: 0.00343 AC XY: 461AN XY: 134498
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GnomAD4 exome AF: 0.00340 AC: 4950AN: 1457744Hom.: 26 Cov.: 32 AF XY: 0.00337 AC XY: 2442AN XY: 725206
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GnomAD4 genome ? AF: 0.00447 AC: 680AN: 152254Hom.: 5 Cov.: 33 AF XY: 0.00424 AC XY: 316AN XY: 74448
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 29, 2018 | - - |
Computational scores
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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