1-26894390-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_022078.3(GPATCH3):​c.897A>C​(p.Glu299Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

Frequency

Genomes: š‘“ 0.0 ( 0 hom., cov: 31)
Failed GnomAD Quality Control

Consequence

GPATCH3
NM_022078.3 missense

Scores

8
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.38
Variant links:
Genes affected
GPATCH3 (HGNC:25720): (G-patch domain containing 3) Predicted to enable nucleic acid binding activity. Involved in negative regulation of RIG-I signaling pathway; negative regulation of type I interferon production; and positive regulation of transcription, DNA-templated. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GPATCH3NM_022078.3 linkc.897A>C p.Glu299Asp missense_variant Exon 3 of 7 ENST00000361720.10 NP_071361.2 Q96I76
GPATCH3XM_047427518.1 linkc.929A>C p.Asn310Thr missense_variant Exon 4 of 4 XP_047283474.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GPATCH3ENST00000361720.10 linkc.897A>C p.Glu299Asp missense_variant Exon 3 of 7 1 NM_022078.3 ENSP00000354645.5 Q96I76

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
152008
Hom.:
0
Cov.:
31
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
152008
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
74254
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.42
BayesDel_addAF
Uncertain
0.020
T
BayesDel_noAF
Benign
-0.21
CADD
Benign
19
DANN
Uncertain
1.0
DEOGEN2
Benign
0.15
T
Eigen
Benign
-0.26
Eigen_PC
Benign
-0.26
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Uncertain
0.91
D
M_CAP
Benign
0.028
D
MetaRNN
Uncertain
0.51
D
MetaSVM
Benign
-0.97
T
MutationAssessor
Uncertain
2.7
M
PrimateAI
Uncertain
0.70
T
PROVEAN
Benign
-2.2
N
REVEL
Benign
0.27
Sift
Benign
0.073
T
Sift4G
Benign
0.11
T
Polyphen
0.45
B
Vest4
0.85
MutPred
0.37
Loss of helix (P = 0.079);
MVP
0.50
MPC
0.50
ClinPred
0.83
D
GERP RS
0.47
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.14
gMVP
0.12

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-27220881; API