chr7-122302848-G-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001024613.4(FEZF1):c.1020C>G(p.Gly340=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000362 in 1,614,068 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00021 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00038 ( 7 hom. )
Consequence
FEZF1
NM_001024613.4 synonymous
NM_001024613.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.302
Genes affected
FEZF1 (HGNC:22788): (FEZ family zinc finger 1) This gene encodes a transcriptional repressor that belongs to the zinc finger double domain protein family. The encoded protein is thought to play a role in the embryonic migration of gonadotropin-releasing hormone neurons into the brain. Mutations in this gene are associated with hypogonadotropic hypogonadism-22 with anosmia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant 7-122302848-G-C is Benign according to our data. Variant chr7-122302848-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1337719.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.302 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FEZF1 | NM_001024613.4 | c.1020C>G | p.Gly340= | synonymous_variant | 3/4 | ENST00000442488.7 | |
FEZF1 | NM_001160264.2 | c.870C>G | p.Gly290= | synonymous_variant | 4/5 | ||
FEZF1 | XM_005250337.4 | c.1020C>G | p.Gly340= | synonymous_variant | 4/5 | ||
FEZF1 | XM_011516202.3 | c.870C>G | p.Gly290= | synonymous_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FEZF1 | ENST00000442488.7 | c.1020C>G | p.Gly340= | synonymous_variant | 3/4 | 1 | NM_001024613.4 | P2 | |
FEZF1 | ENST00000427185.2 | c.870C>G | p.Gly290= | synonymous_variant | 4/5 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000210 AC: 32AN: 152162Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000692 AC: 174AN: 251392Hom.: 1 AF XY: 0.00105 AC XY: 142AN XY: 135866
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GnomAD4 exome AF: 0.000378 AC: 553AN: 1461788Hom.: 7 Cov.: 35 AF XY: 0.000583 AC XY: 424AN XY: 727196
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GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152280Hom.: 1 Cov.: 32 AF XY: 0.000295 AC XY: 22AN XY: 74454
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 19, 2020 | - - |
Computational scores
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Name
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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