chr12-90978265-G-GAAAAAA
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_004950.5(EPYC):c.166-9_166-4dupTTTTTT 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 0.0000074 ( 0 hom., cov: 0)
Consequence
EPYC
NM_004950.5 splice_region, intron
NM_004950.5 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0470
Genes affected
EPYC (HGNC:3053): (epiphycan) Dermatan sulfate proteoglycan 3 is a member of the small leucine-rich repeat proteoglycan family. This gene is composed of seven exons. It regulates fibrillogenesis by interacting with collagen fibrils and other extracellular matrix proteins. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| EPYC | NM_004950.5 | c.166-9_166-4dupTTTTTT | splice_region_variant, intron_variant | Intron 2 of 6 | ENST00000261172.8 | NP_004941.2 | ||
| EPYC | XM_011538008.2 | c.-18-9_-18-4dupTTTTTT | splice_region_variant, intron_variant | Intron 1 of 5 | XP_011536310.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| EPYC | ENST00000261172.8 | c.166-4_166-3insTTTTTT | splice_region_variant, intron_variant | Intron 2 of 6 | 1 | NM_004950.5 | ENSP00000261172.3 | |||
| EPYC | ENST00000551767.1 | c.166-4_166-3insTTTTTT | splice_region_variant, intron_variant | Intron 2 of 4 | 3 | ENSP00000448272.1 | ||||
| EPYC | ENST00000550203.1 | n.70-4_70-3insTTTTTT | splice_region_variant, intron_variant | Intron 1 of 2 | 3 |
Frequencies
GnomAD3 genomes 0.00000745 AC: 1AN: 134306Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
134306
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 Cov.: 0
GnomAD4 exome
Cov.:
0
GnomAD4 genome 0.00000745 AC: 1AN: 134306Hom.: 0 Cov.: 0 AF XY: 0.0000155 AC XY: 1AN XY: 64596 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
134306
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
64596
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
35714
American (AMR)
AF:
AC:
0
AN:
13400
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3280
East Asian (EAS)
AF:
AC:
0
AN:
4658
South Asian (SAS)
AF:
AC:
0
AN:
4148
European-Finnish (FIN)
AF:
AC:
0
AN:
7610
Middle Eastern (MID)
AF:
AC:
0
AN:
290
European-Non Finnish (NFE)
AF:
AC:
0
AN:
62552
Other (OTH)
AF:
AC:
1
AN:
1802
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.325
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
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.