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GeneBe

rs61753370

chr16-574101-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_004204.5(PIGQ):c.27G>A(p.Thr9=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0282 in 1,607,878 control chromosomes in the GnomAD database, including 744 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.019 ( 30 hom., cov: 34)
Exomes 𝑓: 0.029 ( 714 hom. )

Consequence

PIGQ
NM_004204.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.69
Variant links:
Genes affected
PIGQ (HGNC:14135): (phosphatidylinositol glycan anchor biosynthesis class Q) This gene is involved in the first step in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor is a glycolipid found on many blood cells and serves to anchor proteins to the cell surface. This gene encodes a N-acetylglucosaminyl transferase component that is part of the complex that catalyzes transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc to phosphatidylinositol (PI). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 16-574101-G-A is Benign according to our data. Variant chr16-574101-G-A is described in ClinVar as [Benign]. Clinvar id is 456041.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-2.69 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0193 (2940/152324) while in subpopulation NFE AF= 0.0317 (2155/68026). AF 95% confidence interval is 0.0306. There are 30 homozygotes in gnomad4. There are 1342 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 30 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PIGQNM_004204.5 linkuse as main transcriptc.27G>A p.Thr9= synonymous_variant 2/11 ENST00000321878.10
PIGQNM_148920.4 linkuse as main transcriptc.27G>A p.Thr9= synonymous_variant 2/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PIGQENST00000321878.10 linkuse as main transcriptc.27G>A p.Thr9= synonymous_variant 2/111 NM_004204.5 P1Q9BRB3-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0193
AC:
2941
AN:
152206
Hom.:
30
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.00644
Gnomad AMI
AF:
0.0263
Gnomad AMR
AF:
0.0165
Gnomad ASJ
AF:
0.0334
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00331
Gnomad FIN
AF:
0.00584
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.0317
Gnomad OTH
AF:
0.0220
GnomAD3 exomes
AF:
0.0194
AC:
4759
AN:
244746
Hom.:
69
AF XY:
0.0193
AC XY:
2564
AN XY:
133106
show subpopulations
Gnomad AFR exome
AF:
0.00518
Gnomad AMR exome
AF:
0.0113
Gnomad ASJ exome
AF:
0.0384
Gnomad EAS exome
AF:
0.0000547
Gnomad SAS exome
AF:
0.00351
Gnomad FIN exome
AF:
0.00872
Gnomad NFE exome
AF:
0.0317
Gnomad OTH exome
AF:
0.0219
GnomAD4 exome
AF:
0.0292
AC:
42479
AN:
1455554
Hom.:
714
Cov.:
31
AF XY:
0.0284
AC XY:
20596
AN XY:
723956
show subpopulations
Gnomad4 AFR exome
AF:
0.00512
Gnomad4 AMR exome
AF:
0.0117
Gnomad4 ASJ exome
AF:
0.0385
Gnomad4 EAS exome
AF:
0.0000505
Gnomad4 SAS exome
AF:
0.00358
Gnomad4 FIN exome
AF:
0.00969
Gnomad4 NFE exome
AF:
0.0347
Gnomad4 OTH exome
AF:
0.0247
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0193
AC:
2940
AN:
152324
Hom.:
30
Cov.:
34
AF XY:
0.0180
AC XY:
1342
AN XY:
74484
show subpopulations
Gnomad4 AFR
AF:
0.00642
Gnomad4 AMR
AF:
0.0165
Gnomad4 ASJ
AF:
0.0334
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00310
Gnomad4 FIN
AF:
0.00584
Gnomad4 NFE
AF:
0.0317
Gnomad4 OTH
AF:
0.0218
Alfa
AF:
0.0273
Hom.:
21
Bravo
AF:
0.0198
Asia WGS
AF:
0.00231
AC:
8
AN:
3478
EpiCase
AF:
0.0274
EpiControl
AF:
0.0298

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Epilepsy Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeFeb 01, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.61
Cadd
Benign
1.0
Dann
Benign
0.91
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs61753370; hg19: chr16-624101; COSMIC: COSV50314508; COSMIC: COSV50314508; API