rs11083779
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017659.4(QPCTL):c.887-178T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0616 in 152,242 control chromosomes in the GnomAD database, including 382 homozygotes. 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 0.062 ( 382 hom., cov: 31)
Consequence
QPCTL
NM_017659.4 intron
NM_017659.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.805
Publications
8 publications found
Genes affected
QPCTL (HGNC:25952): (glutaminyl-peptide cyclotransferase like) Enables glutaminyl-peptide cyclotransferase activity and zinc ion binding activity. Acts upstream of or within peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
QPCTL | NM_017659.4 | c.887-178T>C | intron_variant | Intron 5 of 6 | ENST00000012049.10 | NP_060129.2 | ||
QPCTL | NM_001163377.2 | c.605-178T>C | intron_variant | Intron 4 of 5 | NP_001156849.1 | |||
QPCTL | XM_047438997.1 | c.787-178T>C | intron_variant | Intron 4 of 4 | XP_047294953.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0616 AC: 9370AN: 152124Hom.: 380 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
9370
AN:
152124
Hom.:
Cov.:
31
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0616 AC: 9378AN: 152242Hom.: 382 Cov.: 31 AF XY: 0.0600 AC XY: 4465AN XY: 74454 show subpopulations
GnomAD4 genome
AF:
AC:
9378
AN:
152242
Hom.:
Cov.:
31
AF XY:
AC XY:
4465
AN XY:
74454
show subpopulations
African (AFR)
AF:
AC:
4491
AN:
41540
American (AMR)
AF:
AC:
479
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
310
AN:
3472
East Asian (EAS)
AF:
AC:
4
AN:
5180
South Asian (SAS)
AF:
AC:
366
AN:
4830
European-Finnish (FIN)
AF:
AC:
385
AN:
10618
Middle Eastern (MID)
AF:
AC:
18
AN:
294
European-Non Finnish (NFE)
AF:
AC:
3212
AN:
68004
Other (OTH)
AF:
AC:
112
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
462
924
1385
1847
2309
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
94
AN:
3478
ClinVar
Not reported inComputational 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
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