rs13385901
Variant names:
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000411678.1(ENSG00000229172):n.1767C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.015 ( 10 hom., cov: 16)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ENSG00000229172
ENST00000411678.1 non_coding_transcript_exon
ENST00000411678.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.501
Publications
1 publications found
Genes affected
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BS2
High Homozygotes in GnomAd4 at 10 gene
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LOC100533842 | n.227803606C>A | intragenic_variant |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ENSG00000229172 | ENST00000411678.1 | n.1767C>A | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 |
Frequencies
GnomAD3 genomes 0.0150 AC: 1351AN: 90310Hom.: 10 Cov.: 16 show subpopulations
GnomAD3 genomes
AF:
AC:
1351
AN:
90310
Hom.:
Cov.:
16
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 Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 70Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 48
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
70
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
48
African (AFR)
AC:
0
AN:
0
American (AMR)
AF:
AC:
0
AN:
2
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2
East Asian (EAS)
AF:
AC:
0
AN:
2
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
0
AN:
58
Other (OTH)
AF:
AC:
0
AN:
6
GnomAD4 genome 0.0150 AC: 1353AN: 90310Hom.: 10 Cov.: 16 AF XY: 0.0164 AC XY: 708AN XY: 43180 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1353
AN:
90310
Hom.:
Cov.:
16
AF XY:
AC XY:
708
AN XY:
43180
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
499
AN:
23548
American (AMR)
AF:
AC:
149
AN:
7942
Ashkenazi Jewish (ASJ)
AF:
AC:
23
AN:
2438
East Asian (EAS)
AF:
AC:
69
AN:
3384
South Asian (SAS)
AF:
AC:
73
AN:
2060
European-Finnish (FIN)
AF:
AC:
110
AN:
4748
Middle Eastern (MID)
AF:
AC:
1
AN:
216
European-Non Finnish (NFE)
AF:
AC:
407
AN:
44046
Other (OTH)
AF:
AC:
17
AN:
1256
⚠️ 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: 0.361
Heterozygous variant carriers
0
59
118
176
235
294
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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