rs140497485

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001002909.4(GPATCH8):​c.3473A>G​(p.Asn1158Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000111 in 1,550,192 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.00053 ( 0 hom., cov: 32)
Exomes š‘“: 0.000065 ( 0 hom. )

Consequence

GPATCH8
NM_001002909.4 missense

Scores

16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.325
Variant links:
Genes affected
GPATCH8 (HGNC:29066): (G-patch domain containing 8) The protein encoded by this gene contains an RNA-processing domain, a zinc finger domain, a lysine-rich region and a serine-rich region. A mutation in the serine-rich region of the protein is thought to be associated with hyperuricemia (PMID: 21594610). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2015]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.0045214593).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GPATCH8NM_001002909.4 linkc.3473A>G p.Asn1158Ser missense_variant Exon 8 of 8 ENST00000591680.6 NP_001002909.1 Q9UKJ3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GPATCH8ENST00000591680.6 linkc.3473A>G p.Asn1158Ser missense_variant Exon 8 of 8 2 NM_001002909.4 ENSP00000467556.1 Q9UKJ3-1

Frequencies

GnomAD3 genomes
AF:
0.000532
AC:
81
AN:
152148
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00188
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000212
AC:
41
AN:
193736
Hom.:
0
AF XY:
0.000195
AC XY:
20
AN XY:
102644
show subpopulations
Gnomad AFR exome
AF:
0.00242
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000242
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000651
AC:
91
AN:
1397926
Hom.:
0
Cov.:
34
AF XY:
0.0000580
AC XY:
40
AN XY:
689700
show subpopulations
Gnomad4 AFR exome
AF:
0.00241
Gnomad4 AMR exome
AF:
0.0000291
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000508
Gnomad4 SAS exome
AF:
0.0000543
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000461
Gnomad4 OTH exome
AF:
0.0000695
GnomAD4 genome
AF:
0.000532
AC:
81
AN:
152266
Hom.:
0
Cov.:
32
AF XY:
0.000457
AC XY:
34
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.00188
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000144
Hom.:
0
Bravo
AF:
0.000665
ESP6500AA
AF:
0.00204
AC:
9
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000182
AC:
22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.051
BayesDel_addAF
Benign
-0.73
T
BayesDel_noAF
Benign
-0.83
CADD
Benign
5.2
DANN
Benign
0.79
DEOGEN2
Benign
0.022
T
Eigen
Benign
-0.80
Eigen_PC
Benign
-0.69
FATHMM_MKL
Benign
0.27
N
LIST_S2
Benign
0.51
T
M_CAP
Benign
0.0068
T
MetaRNN
Benign
0.0045
T
MetaSVM
Benign
-0.94
T
MutationAssessor
Benign
0.63
N
PrimateAI
Benign
0.35
T
Sift4G
Benign
0.34
T
Polyphen
0.0010
B
Vest4
0.063
MVP
0.043
MPC
0.11
ClinPred
0.0041
T
GERP RS
1.5
Varity_R
0.024
gMVP
0.041

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: rs140497485; hg19: chr17-42475972; API