chr5-138466962-G-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001964.3(EGR1):c.513G>C(p.Ser171=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00249 in 1,613,892 control chromosomes in the GnomAD database, including 75 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 44 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 31 hom. )
Consequence
EGR1
NM_001964.3 synonymous
NM_001964.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.63
Genes affected
EGR1 (HGNC:3238): (early growth response 1) The protein encoded by this gene belongs to the EGR family of C2H2-type zinc-finger proteins. It is a nuclear protein and functions as a transcriptional regulator. The products of target genes it activates are required for differentitation and mitogenesis. Studies suggest this is a cancer suppressor gene. [provided by RefSeq, Dec 2014]
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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=-0.88).
BP6
?
Variant 5-138466962-G-C is Benign according to our data. Variant chr5-138466962-G-C is described in ClinVar as [Benign]. Clinvar id is 768032.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.63 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0133 (2016/152072) while in subpopulation AFR AF= 0.0462 (1915/41440). AF 95% confidence interval is 0.0445. There are 44 homozygotes in gnomad4. There are 951 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2011 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EGR1 | NM_001964.3 | c.513G>C | p.Ser171= | synonymous_variant | 2/2 | ENST00000239938.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EGR1 | ENST00000239938.5 | c.513G>C | p.Ser171= | synonymous_variant | 2/2 | 1 | NM_001964.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0132 AC: 2011AN: 151954Hom.: 44 Cov.: 32
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GnomAD3 exomes AF: 0.00361 AC: 908AN: 251344Hom.: 12 AF XY: 0.00273 AC XY: 371AN XY: 135852
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GnomAD4 exome AF: 0.00137 AC: 2000AN: 1461820Hom.: 31 Cov.: 33 AF XY: 0.00119 AC XY: 867AN XY: 727216
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GnomAD4 genome ? AF: 0.0133 AC: 2016AN: 152072Hom.: 44 Cov.: 32 AF XY: 0.0128 AC XY: 951AN XY: 74354
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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 | Aug 18, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at