NM_015122.3:c.6G>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_015122.3(FCHO1):c.6G>T(p.Ser2Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,458,932 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: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
FCHO1
NM_015122.3 synonymous
NM_015122.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.55
Publications
0 publications found
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]
FCHO1 Gene-Disease associations (from GenCC):
- immunodeficiency 76Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 19-17755170-G-T is Benign according to our data. Variant chr19-17755170-G-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2035885.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.55 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_015122.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FCHO1 | NM_015122.3 | MANE Select | c.6G>T | p.Ser2Ser | synonymous | Exon 4 of 29 | NP_055937.1 | O14526-1 | |
| FCHO1 | NM_001161357.2 | c.6G>T | p.Ser2Ser | synonymous | Exon 4 of 29 | NP_001154829.1 | A0A0C3SFZ9 | ||
| FCHO1 | NM_001161358.2 | c.6G>T | p.Ser2Ser | synonymous | Exon 3 of 28 | NP_001154830.1 | O14526-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FCHO1 | ENST00000596536.6 | TSL:5 MANE Select | c.6G>T | p.Ser2Ser | synonymous | Exon 4 of 29 | ENSP00000470731.1 | O14526-1 | |
| FCHO1 | ENST00000699212.1 | c.6G>T | p.Ser2Ser | synonymous | Exon 4 of 30 | ENSP00000514208.1 | A0A8V8TPN1 | ||
| FCHO1 | ENST00000594202.6 | TSL:5 | c.6G>T | p.Ser2Ser | synonymous | Exon 4 of 29 | ENSP00000473001.1 | A0A0C3SFZ9 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1458932Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 725822 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1458932
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
725822
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33282
American (AMR)
AF:
AC:
0
AN:
43942
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25938
East Asian (EAS)
AF:
AC:
0
AN:
39572
South Asian (SAS)
AF:
AC:
0
AN:
85978
European-Finnish (FIN)
AF:
AC:
0
AN:
53364
Middle Eastern (MID)
AF:
AC:
0
AN:
5752
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1110848
Other (OTH)
AF:
AC:
0
AN:
60256
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.