19-17762800-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_015122.3(FCHO1):c.66C>T(p.Ser22Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,912 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
FCHO1
NM_015122.3 synonymous
NM_015122.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.628
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
Variant 19-17762800-C-T is Benign according to our data. Variant chr19-17762800-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1574977.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.628 with no splicing effect.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FCHO1 | ENST00000596536.6 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 5 of 29 | 5 | NM_015122.3 | ENSP00000470731.1 | ||
FCHO1 | ENST00000699212.1 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 5 of 30 | ENSP00000514208.1 | ||||
FCHO1 | ENST00000594202.6 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 5 of 29 | 5 | ENSP00000473001.1 | |||
FCHO1 | ENST00000596309.6 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 5 of 29 | 4 | ENSP00000470511.2 | |||
FCHO1 | ENST00000596951.6 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 5 of 29 | 5 | ENSP00000472417.1 | |||
FCHO1 | ENST00000600209.6 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 5 of 29 | 5 | ENSP00000469075.2 | |||
FCHO1 | ENST00000600676.5 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 4 of 28 | 2 | ENSP00000470493.1 | |||
FCHO1 | ENST00000699176.1 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 5 of 29 | ENSP00000514179.1 | ||||
FCHO1 | ENST00000699177.1 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 5 of 29 | ENSP00000514180.1 | ||||
FCHO1 | ENST00000699207.1 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 5 of 29 | ENSP00000514204.1 | ||||
FCHO1 | ENST00000699209.1 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 5 of 29 | ENSP00000514206.1 | ||||
FCHO1 | ENST00000699215.1 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 4 of 28 | ENSP00000514211.1 | ||||
FCHO1 | ENST00000699202.1 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 5 of 29 | ENSP00000514200.1 | ||||
FCHO1 | ENST00000699214.1 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 4 of 28 | ENSP00000514210.1 | ||||
FCHO1 | ENST00000699208.1 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 5 of 28 | ENSP00000514205.1 | ||||
FCHO1 | ENST00000699198.1 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 5 of 29 | ENSP00000514196.1 | ||||
FCHO1 | ENST00000699199.1 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 4 of 28 | ENSP00000514197.1 | ||||
FCHO1 | ENST00000699213.1 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 4 of 28 | ENSP00000514209.1 | ||||
FCHO1 | ENST00000699197.1 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 5 of 28 | ENSP00000514195.1 | ||||
FCHO1 | ENST00000699200.1 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 5 of 28 | ENSP00000514198.1 | ||||
FCHO1 | ENST00000699196.1 | c.66C>T | p.Ser22Ser | synonymous_variant | Exon 5 of 27 | ENSP00000514194.1 | ||||
FCHO1 | ENST00000699203 | c.-85C>T | 5_prime_UTR_variant | Exon 3 of 22 | ENSP00000514201.1 | |||||
FCHO1 | ENST00000699201.1 | n.66C>T | non_coding_transcript_exon_variant | Exon 5 of 28 | ENSP00000514199.1 | |||||
FCHO1 | ENST00000699205.1 | n.66C>T | non_coding_transcript_exon_variant | Exon 5 of 27 | ENSP00000514202.1 | |||||
FCHO1 | ENST00000699206.1 | n.66C>T | non_coding_transcript_exon_variant | Exon 5 of 29 | ENSP00000514203.1 | |||||
FCHO1 | ENST00000699210.1 | n.66C>T | non_coding_transcript_exon_variant | Exon 5 of 28 | ENSP00000514207.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152142Hom.: 0 Cov.: 31
GnomAD3 genomes
AF:
AC:
1
AN:
152142
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251454Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135894
GnomAD3 exomes
AF:
AC:
1
AN:
251454
Hom.:
AF XY:
AC XY:
1
AN XY:
135894
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461770Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727200
GnomAD4 exome
AF:
AC:
1
AN:
1461770
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
727200
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152142Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74324
GnomAD4 genome
AF:
AC:
1
AN:
152142
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
74324
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Aug 27, 2021
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at