X-132077878-TA-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM4BP6_ModerateBS2
The NM_194277.3(FRMD7):c.2138del(p.Leu713Ter) variant causes a frameshift change. The variant allele was found at a frequency of 0.0000885 in 1,209,216 control chromosomes in the GnomAD database, including 1 homozygotes. There are 31 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000071 ( 0 hom., 4 hem., cov: 23)
Exomes 𝑓: 0.000090 ( 1 hom. 27 hem. )
Consequence
FRMD7
NM_194277.3 frameshift
NM_194277.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.85
Genes affected
FRMD7 (HGNC:8079): (FERM domain containing 7) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of neuron projection development. Predicted to act upstream of or within several processes, including negative regulation of stress fiber assembly; positive regulation of lamellipodium assembly; and positive regulation of small GTPase mediated signal transduction. Located in cytosol; nucleoplasm; and plasma membrane. Implicated in congenital nystagmus 1. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM4
?
Frameshift in the end of transcript resulting in stoplost. Downstream stopcodon found after 769 codons.
BP6
?
Variant X-132077878-TA-T is Benign according to our data. Variant chrX-132077878-TA-T is described in ClinVar as [Benign]. Clinvar id is 789255.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Hemizygotes in GnomAd at 4 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRMD7 | NM_194277.3 | c.2138del | p.Leu713Ter | frameshift_variant | 12/12 | ENST00000298542.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRMD7 | ENST00000298542.9 | c.2138del | p.Leu713Ter | frameshift_variant | 12/12 | 1 | NM_194277.3 | P1 | |
FRMD7 | ENST00000464296.1 | c.2093del | p.Leu698Ter | frameshift_variant | 12/12 | 1 | |||
FRMD7 | ENST00000370879.5 | c.1778del | p.Leu593Ter | frameshift_variant | 8/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000711 AC: 8AN: 112526Hom.: 0 Cov.: 23 AF XY: 0.000115 AC XY: 4AN XY: 34670
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GnomAD3 exomes AF: 0.0000711 AC: 13AN: 182757Hom.: 0 AF XY: 0.0000445 AC XY: 3AN XY: 67453
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GnomAD4 exome AF: 0.0000903 AC: 99AN: 1096690Hom.: 1 Cov.: 29 AF XY: 0.0000746 AC XY: 27AN XY: 362104
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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 18, 2023 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at