X-47639035-G-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001114123.3(ELK1):āc.514C>Gā(p.Pro172Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000801 in 1,202,537 control chromosomes in the GnomAD database, including 3 homozygotes. There are 277 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0046 ( 1 hom., 143 hem., cov: 23)
Exomes š: 0.00041 ( 2 hom. 134 hem. )
Consequence
ELK1
NM_001114123.3 missense
NM_001114123.3 missense
Scores
2
13
Clinical Significance
Conservation
PhyloP100: 3.72
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.004161954).
BP6
Variant X-47639035-G-C is Benign according to our data. Variant chrX-47639035-G-C is described in ClinVar as [Benign]. Clinvar id is 714925.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Hemizygotes in GnomAd4 at 143 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELK1 | NM_001114123.3 | c.514C>G | p.Pro172Ala | missense_variant | 4/7 | ENST00000376983.8 | |
ELK1 | NM_005229.4 | c.514C>G | p.Pro172Ala | missense_variant | 3/6 | ||
ELK1 | NM_001257168.1 | c.270+244C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELK1 | ENST00000376983.8 | c.514C>G | p.Pro172Ala | missense_variant | 4/7 | 1 | NM_001114123.3 | P1 | |
ELK1 | ENST00000247161.7 | c.514C>G | p.Pro172Ala | missense_variant | 3/6 | 1 | P1 | ||
ELK1 | ENST00000343894.8 | c.270+244C>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00458 AC: 517AN: 112882Hom.: 1 Cov.: 23 AF XY: 0.00406 AC XY: 142AN XY: 35014
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GnomAD3 exomes AF: 0.00128 AC: 206AN: 161064Hom.: 2 AF XY: 0.000857 AC XY: 45AN XY: 52538
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GnomAD4 exome AF: 0.000409 AC: 446AN: 1089600Hom.: 2 Cov.: 33 AF XY: 0.000375 AC XY: 134AN XY: 357108
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GnomAD4 genome AF: 0.00458 AC: 517AN: 112937Hom.: 1 Cov.: 23 AF XY: 0.00408 AC XY: 143AN XY: 35079
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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 | Dec 28, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
N;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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