rs751227407
Your query was ambiguous. Multiple possible variants found:
- chr1-165743318-GAAAAAAA-G
- chr1-165743318-GAAAAAAA-GAAA
- chr1-165743318-GAAAAAAA-GAAAA
- chr1-165743318-GAAAAAAA-GAAAAA
- chr1-165743318-GAAAAAAA-GAAAAAA
- chr1-165743318-GAAAAAAA-GAAAAAAAA
- chr1-165743318-GAAAAAAA-GAAAAAAAAA
- chr1-165743318-GAAAAAAA-GAAAAAAAAAA
- chr1-165743318-GAAAAAAA-GAAAAAAAAAAA
- chr1-165743318-GAAAAAAA-GAAAAAAAAAAAA
- chr1-165743318-GAAAAAAA-GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
- chr1-165743318-GAAAAAAA-GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
- chr1-165743318-GAAAAAAA-GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_019026.6(TMCO1):c.324-14_324-8delTTTTTTT variant causes a splice region, intron change. The variant allele was found at a frequency of 0.0000016 in 1,252,592 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000016 ( 0 hom. )
Consequence
TMCO1
NM_019026.6 splice_region, intron
NM_019026.6 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.89
Publications
0 publications found
Genes affected
TMCO1 (HGNC:18188): (transmembrane and coiled-coil domains 1) This locus encodes a transmembrane protein. Mutations at this locus have been associated with craniofacial dysmorphism, skeletal anomalies, and cognitive disability. Mutations at this locus have also been associated with open angle glaucoma blindness. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2012]
TMCO1 Gene-Disease associations (from GenCC):
- cerebrofaciothoracic dysplasiaInheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, Illumina, Laboratory for Molecular Medicine, Orphanet
- craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development 1Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, G2P
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_019026.6. 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 |
|---|---|---|---|---|---|---|---|---|---|
| TMCO1 | MANE Select | c.324-14_324-8delTTTTTTT | splice_region intron | N/A | NP_061899.3 | Q9UM00-1 | |||
| TMCO1 | c.375-14_375-8delTTTTTTT | splice_region intron | N/A | NP_001243093.1 | B7Z591 | ||||
| TMCO1 | c.288-14_288-8delTTTTTTT | splice_region intron | N/A | NP_001243094.1 | B7Z591 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TMCO1 | TSL:1 MANE Select | c.324-14_324-8delTTTTTTT | splice_region intron | N/A | ENSP00000356856.6 | Q9UM00-1 | |||
| TMCO1 | TSL:1 | c.477-14_477-8delTTTTTTT | splice_region intron | N/A | ENSP00000480514.1 | Q9UM00-3 | |||
| TMCO1 | c.447-14_447-8delTTTTTTT | splice_region intron | N/A | ENSP00000538522.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000160 AC: 2AN: 1252592Hom.: 0 AF XY: 0.00000319 AC XY: 2AN XY: 627072 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1252592
Hom.:
AF XY:
AC XY:
2
AN XY:
627072
show subpopulations
African (AFR)
AF:
AC:
0
AN:
27894
American (AMR)
AF:
AC:
0
AN:
37084
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
22992
East Asian (EAS)
AF:
AC:
0
AN:
35862
South Asian (SAS)
AF:
AC:
0
AN:
75188
European-Finnish (FIN)
AF:
AC:
0
AN:
48122
Middle Eastern (MID)
AF:
AC:
0
AN:
4346
European-Non Finnish (NFE)
AF:
AC:
2
AN:
948836
Other (OTH)
AF:
AC:
0
AN:
52268
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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