rs2230299

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_012413.4(QPCT):​c.126C>T​(p.Tyr42=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0969 in 1,613,298 control chromosomes in the GnomAD database, including 19,126 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 0.21 ( 6218 hom., cov: 33)
Exomes 𝑓: 0.085 ( 12908 hom. )

Consequence

QPCT
NM_012413.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.143
Variant links:
Genes affected
QPCT (HGNC:9753): (glutaminyl-peptide cyclotransferase) This gene encodes human pituitary glutaminyl cyclase, which is responsible for the presence of pyroglutamyl residues in many neuroendocrine peptides. The amino acid sequence of this enzyme is 86% identical to that of bovine glutaminyl cyclase. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP7
Synonymous conserved (PhyloP=0.143 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
QPCTNM_012413.4 linkuse as main transcriptc.126C>T p.Tyr42= synonymous_variant 2/7 ENST00000338415.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
QPCTENST00000338415.8 linkuse as main transcriptc.126C>T p.Tyr42= synonymous_variant 2/71 NM_012413.4 P1Q16769-1
QPCTENST00000650442.1 linkuse as main transcriptc.-67C>T 5_prime_UTR_variant 2/4
QPCTENST00000404976.5 linkuse as main transcriptc.121-6786C>T intron_variant 2
QPCTENST00000470075.1 linkuse as main transcriptn.130C>T non_coding_transcript_exon_variant 2/43

Frequencies

GnomAD3 genomes
AF:
0.211
AC:
32042
AN:
152048
Hom.:
6205
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.488
Gnomad AMI
AF:
0.00768
Gnomad AMR
AF:
0.271
Gnomad ASJ
AF:
0.105
Gnomad EAS
AF:
0.347
Gnomad SAS
AF:
0.132
Gnomad FIN
AF:
0.113
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.0482
Gnomad OTH
AF:
0.196
GnomAD3 exomes
AF:
0.164
AC:
41164
AN:
251294
Hom.:
6485
AF XY:
0.144
AC XY:
19590
AN XY:
135824
show subpopulations
Gnomad AFR exome
AF:
0.497
Gnomad AMR exome
AF:
0.390
Gnomad ASJ exome
AF:
0.106
Gnomad EAS exome
AF:
0.338
Gnomad SAS exome
AF:
0.119
Gnomad FIN exome
AF:
0.108
Gnomad NFE exome
AF:
0.0492
Gnomad OTH exome
AF:
0.129
GnomAD4 exome
AF:
0.0850
AC:
124148
AN:
1461132
Hom.:
12908
Cov.:
31
AF XY:
0.0831
AC XY:
60409
AN XY:
726770
show subpopulations
Gnomad4 AFR exome
AF:
0.500
Gnomad4 AMR exome
AF:
0.371
Gnomad4 ASJ exome
AF:
0.103
Gnomad4 EAS exome
AF:
0.341
Gnomad4 SAS exome
AF:
0.119
Gnomad4 FIN exome
AF:
0.111
Gnomad4 NFE exome
AF:
0.0458
Gnomad4 OTH exome
AF:
0.117
GnomAD4 genome
AF:
0.211
AC:
32110
AN:
152166
Hom.:
6218
Cov.:
33
AF XY:
0.213
AC XY:
15838
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.488
Gnomad4 AMR
AF:
0.271
Gnomad4 ASJ
AF:
0.105
Gnomad4 EAS
AF:
0.347
Gnomad4 SAS
AF:
0.131
Gnomad4 FIN
AF:
0.113
Gnomad4 NFE
AF:
0.0483
Gnomad4 OTH
AF:
0.197
Alfa
AF:
0.109
Hom.:
1375
Bravo
AF:
0.241
Asia WGS
AF:
0.235
AC:
816
AN:
3478
EpiCase
AF:
0.0476
EpiControl
AF:
0.0462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
1.7
DANN
Benign
0.31

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2230299; hg19: chr2-37579937; COSMIC: COSV58119314; API