19-3543480-GCCCCCC-GCCCCCCCCCCCCCCCC
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The ENST00000329493.6(TEKTIP1):c.322+7_322+8insCCCCCCCCCC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000032 ( 0 hom., cov: 0)
Exomes 𝑓: 8.2e-7 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TEKTIP1
ENST00000329493.6 splice_region, intron
ENST00000329493.6 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.478
Publications
0 publications found
Genes affected
TEKTIP1 (HGNC:34496): (tektin bundle interacting protein 1)
MFSD12 (HGNC:28299): (major facilitator superfamily domain containing 12) Enables cysteine transmembrane transporter activity. Involved in cysteine transmembrane transport; pigment metabolic process involved in pigmentation; and regulation of melanin biosynthetic process. Located in lysosome and melanosome. Part of late endosome. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
new If you want to explore the variant's impact on the transcript ENST00000329493.6, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: ENST00000329493.6. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TEKTIP1 | TSL:2 MANE Select | c.322+7_322+8insCCCCCCCCCC | splice_region intron | N/A | ENSP00000327950.4 | A6NCJ1 | |||
| MFSD12 | TSL:2 | c.329-504_329-503insGGGGGGGGGG | intron | N/A | ENSP00000381566.4 | A0A0A0MS91 | |||
| MFSD12 | TSL:3 | c.490+1328_490+1329insGGGGGGGGGG | intron | N/A | ENSP00000478456.1 | A0A087WU85 |
Frequencies
GnomAD3 genomes 0.0000325 AC: 4AN: 123130Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
4
AN:
123130
Hom.:
Cov.:
0
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:
GnomAD4 exome AF: 8.23e-7 AC: 1AN: 1215596Hom.: 0 Cov.: 0 AF XY: 0.00000167 AC XY: 1AN XY: 599434 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
1215596
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
599434
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
28154
American (AMR)
AF:
AC:
0
AN:
33012
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
22134
East Asian (EAS)
AF:
AC:
0
AN:
33838
South Asian (SAS)
AF:
AC:
0
AN:
71462
European-Finnish (FIN)
AF:
AC:
0
AN:
37934
Middle Eastern (MID)
AF:
AC:
0
AN:
3624
European-Non Finnish (NFE)
AF:
AC:
1
AN:
933780
Other (OTH)
AF:
AC:
0
AN:
51658
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.275
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 0.0000325 AC: 4AN: 123130Hom.: 0 Cov.: 0 AF XY: 0.0000338 AC XY: 2AN XY: 59126 show subpopulations
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
4
AN:
123130
Hom.:
Cov.:
0
AF XY:
AC XY:
2
AN XY:
59126
show subpopulations
African (AFR)
AF:
AC:
3
AN:
29872
American (AMR)
AF:
AC:
0
AN:
12554
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3092
East Asian (EAS)
AF:
AC:
0
AN:
4662
South Asian (SAS)
AF:
AC:
0
AN:
3662
European-Finnish (FIN)
AF:
AC:
0
AN:
7600
Middle Eastern (MID)
AF:
AC:
0
AN:
226
European-Non Finnish (NFE)
AF:
AC:
1
AN:
59092
Other (OTH)
AF:
AC:
0
AN:
1652
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.688
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.
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.