chr6-142367704-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198569.3(ADGRG6):āc.239A>Gā(p.Gln80Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000366 in 1,613,814 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 32)
Exomes š: 0.000040 ( 0 hom. )
Consequence
ADGRG6
NM_198569.3 missense
NM_198569.3 missense
Scores
4
14
Clinical Significance
Conservation
PhyloP100: 4.99
Genes affected
ADGRG6 (HGNC:13841): (adhesion G protein-coupled receptor G6) This gene, which is upregulated in human umbilical vein endothelial cells, encodes a G protein-coupled receptor. Variations in this gene can affect a person's stature. Multiple transcript variants encoding different proteins have been found for this gene. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.21103147).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADGRG6 | NM_198569.3 | c.239A>G | p.Gln80Arg | missense_variant | 3/25 | ENST00000367609.8 | NP_940971.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADGRG6 | ENST00000367609.8 | c.239A>G | p.Gln80Arg | missense_variant | 3/25 | 1 | NM_198569.3 | ENSP00000356581 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000442 AC: 11AN: 249136Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135150
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GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461622Hom.: 0 Cov.: 32 AF XY: 0.0000371 AC XY: 27AN XY: 727096
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74354
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 22, 2022 | The c.239A>G (p.Q80R) alteration is located in exon 3 (coding exon 3) of the ADGRG6 gene. This alteration results from a A to G substitution at nucleotide position 239, causing the glutamine (Q) at amino acid position 80 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;.;.;T;.
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N
REVEL
Benign
Sift
Benign
T;D;D;T;T;T
Sift4G
Benign
.;.;.;.;T;T
Polyphen
B;B;B;B;B;.
Vest4
MutPred
Gain of phosphorylation at T82 (P = 0.1505);Gain of phosphorylation at T82 (P = 0.1505);Gain of phosphorylation at T82 (P = 0.1505);Gain of phosphorylation at T82 (P = 0.1505);.;Gain of phosphorylation at T82 (P = 0.1505);
MVP
MPC
0.16
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at