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GeneBe

rs560887

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021176(G6PC2):c.441-26T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152034 control chromosomes in the gnomAD Genomes database, including 49694 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 0.80 ( 49694 hom., cov: 31)
Exomes 𝑓: 0.79 ( 79660 hom. )

Consequence

G6PC2
NM_021176 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.88

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
G6PC2NM_021176.3 linkuse as main transcriptc.441-26T>C intron_variant ENST00000375363.8
G6PC2NM_001081686.2 linkuse as main transcriptc.441-930T>C intron_variant
G6PC2XM_011511564.4 linkuse as main transcriptc.329-930T>C intron_variant
G6PC2XM_011511565.4 linkuse as main transcriptc.93-26T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
G6PC2ENST00000375363.8 linkuse as main transcriptc.441-26T>C intron_variant 1 NM_021176.3 P1Q9NQR9-1

Frequencies

GnomAD3 genomes
AF:
0.801
AC:
121709
AN:
152034
Hom.:
49694
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.947
Gnomad AMI
AF:
0.780
Gnomad AMR
AF:
0.812
Gnomad ASJ
AF:
0.793
Gnomad EAS
AF:
0.966
Gnomad SAS
AF:
0.885
Gnomad FIN
AF:
0.708
Gnomad MID
AF:
0.763
Gnomad NFE
AF:
0.705
Gnomad OTH
AF:
0.794
GnomAD3 exomes
AF:
0.790
AC:
198206
AN:
250980
Hom.:
79660
AF XY:
0.784
AC XY:
106450
AN XY:
135692
show subpopulations
Gnomad AFR exome
AF:
0.951
Gnomad AMR exome
AF:
0.876
Gnomad ASJ exome
AF:
0.805
Gnomad EAS exome
AF:
0.967
Gnomad SAS exome
AF:
0.875
Gnomad FIN exome
AF:
0.702
Gnomad NFE exome
AF:
0.705
Gnomad OTH exome
AF:
0.756
GnomAD4 exome
AF:
0.748
AC:
728381
AN:
974384
Hom.:
276243
AF XY:
0.751
AC XY:
379924
AN XY:
506166
show subpopulations
Gnomad4 AFR exome
AF:
0.953
Gnomad4 AMR exome
AF:
0.870
Gnomad4 ASJ exome
AF:
0.813
Gnomad4 EAS exome
AF:
0.971
Gnomad4 SAS exome
AF:
0.872
Gnomad4 FIN exome
AF:
0.698
Gnomad4 NFE exome
AF:
0.705
Gnomad4 OTH exome
AF:
0.767
Alfa
AF:
0.732
Hom.:
84882
Bravo
AF:
0.816
Asia WGS
AF:
0.916
AC:
3185
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
Cadd
Benign
0.21
Dann
Benign
0.74

Splicing

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: rs560887; hg19: chr2-169763148;