chr19-17762730-C-T
Position:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_015122.3(FCHO1):c.28-32C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00548 in 1,503,916 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0032 ( 1 hom., cov: 31)
Exomes 𝑓: 0.0057 ( 38 hom. )
Consequence
FCHO1
NM_015122.3 intron
NM_015122.3 intron
Scores
9
Clinical Significance
Conservation
PhyloP100: -0.140
Genes affected
FCHO1 (HGNC:29002): (FCH and mu domain containing endocytic adaptor 1) Enables AP-2 adaptor complex binding activity. Involved in clathrin coat assembly and clathrin-dependent endocytosis. Located in cytosol; nucleoplasm; and plasma membrane. Is active in clathrin-coated pit. Implicated in primary immunodeficiency disease. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0048695803).
BP6
Variant 19-17762730-C-T is Benign according to our data. Variant chr19-17762730-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2649554.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00317 (483/152280) while in subpopulation NFE AF= 0.00545 (371/68026). AF 95% confidence interval is 0.005. There are 1 homozygotes in gnomad4. There are 214 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 38 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FCHO1 | NM_015122.3 | c.28-32C>T | intron_variant | ENST00000596536.6 | NP_055937.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FCHO1 | ENST00000596536.6 | c.28-32C>T | intron_variant | 5 | NM_015122.3 | ENSP00000470731.1 | ||||
FCHO1 | ENST00000699212.1 | c.28-32C>T | intron_variant | ENSP00000514208.1 | ||||||
FCHO1 | ENST00000594202.6 | c.28-32C>T | intron_variant | 5 | ENSP00000473001.1 | |||||
FCHO1 | ENST00000596309.6 | c.28-32C>T | intron_variant | 4 | ENSP00000470511.2 | |||||
FCHO1 | ENST00000596951.6 | c.28-32C>T | intron_variant | 5 | ENSP00000472417.1 | |||||
FCHO1 | ENST00000600209.6 | c.28-32C>T | intron_variant | 5 | ENSP00000469075.2 | |||||
FCHO1 | ENST00000600676.5 | c.28-32C>T | intron_variant | 2 | ENSP00000470493.1 | |||||
FCHO1 | ENST00000699176.1 | c.28-32C>T | intron_variant | ENSP00000514179.1 | ||||||
FCHO1 | ENST00000699177.1 | c.28-32C>T | intron_variant | ENSP00000514180.1 | ||||||
FCHO1 | ENST00000699207.1 | c.28-32C>T | intron_variant | ENSP00000514204.1 | ||||||
FCHO1 | ENST00000699209.1 | c.28-32C>T | intron_variant | ENSP00000514206.1 | ||||||
FCHO1 | ENST00000699215.1 | c.28-32C>T | intron_variant | ENSP00000514211.1 | ||||||
FCHO1 | ENST00000699202.1 | c.28-32C>T | intron_variant | ENSP00000514200.1 | ||||||
FCHO1 | ENST00000699214.1 | c.28-32C>T | intron_variant | ENSP00000514210.1 | ||||||
FCHO1 | ENST00000699208.1 | c.28-32C>T | intron_variant | ENSP00000514205.1 | ||||||
FCHO1 | ENST00000699198.1 | c.28-32C>T | intron_variant | ENSP00000514196.1 | ||||||
FCHO1 | ENST00000699199.1 | c.28-32C>T | intron_variant | ENSP00000514197.1 | ||||||
FCHO1 | ENST00000699213.1 | c.28-32C>T | intron_variant | ENSP00000514209.1 | ||||||
FCHO1 | ENST00000699197.1 | c.28-32C>T | intron_variant | ENSP00000514195.1 | ||||||
FCHO1 | ENST00000699200.1 | c.28-32C>T | intron_variant | ENSP00000514198.1 | ||||||
FCHO1 | ENST00000699196.1 | c.28-32C>T | intron_variant | ENSP00000514194.1 | ||||||
FCHO1 | ENST00000699203.1 | c.-123-32C>T | intron_variant | ENSP00000514201.1 | ||||||
FCHO1 | ENST00000699201.1 | n.28-32C>T | intron_variant | ENSP00000514199.1 | ||||||
FCHO1 | ENST00000699205.1 | n.28-32C>T | intron_variant | ENSP00000514202.1 | ||||||
FCHO1 | ENST00000699206.1 | n.28-32C>T | intron_variant | ENSP00000514203.1 | ||||||
FCHO1 | ENST00000699210.1 | n.28-32C>T | intron_variant | ENSP00000514207.1 |
Frequencies
GnomAD3 genomes AF: 0.00317 AC: 483AN: 152162Hom.: 1 Cov.: 31
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GnomAD3 exomes AF: 0.00354 AC: 891AN: 251360Hom.: 6 AF XY: 0.00379 AC XY: 515AN XY: 135848
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GnomAD4 exome AF: 0.00574 AC: 7758AN: 1351636Hom.: 38 Cov.: 22 AF XY: 0.00578 AC XY: 3926AN XY: 678988
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GnomAD4 genome AF: 0.00317 AC: 483AN: 152280Hom.: 1 Cov.: 31 AF XY: 0.00287 AC XY: 214AN XY: 74450
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | FCHO1: BS2 - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
Sift4G
Benign
T
Vest4
MVP
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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