chr17-18107222-C-T
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_001388.5(DRG2):c.1077C>T(p.Ile359=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00526 in 1,613,272 control chromosomes in the GnomAD database, including 396 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.028 ( 203 hom., cov: 32)
Exomes 𝑓: 0.0029 ( 193 hom. )
Consequence
DRG2
NM_001388.5 synonymous
NM_001388.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.48
Genes affected
DRG2 (HGNC:3030): (developmentally regulated GTP binding protein 2) This gene encodes a GTP-binding protein known to function in the regulation of cell growth and differentiation. Read-through transcripts containing this gene and a downstream gene have been identified, but they are not thought to encode a fusion protein. This gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BP6
Variant 17-18107222-C-T is Benign according to our data. Variant chr17-18107222-C-T is described in ClinVar as [Benign]. Clinvar id is 768839.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.48 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0929 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DRG2 | NM_001388.5 | c.1077C>T | p.Ile359= | synonymous_variant | 13/13 | ENST00000225729.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DRG2 | ENST00000225729.8 | c.1077C>T | p.Ile359= | synonymous_variant | 13/13 | 1 | NM_001388.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0275 AC: 4181AN: 152212Hom.: 202 Cov.: 32
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GnomAD3 exomes AF: 0.00750 AC: 1875AN: 249898Hom.: 97 AF XY: 0.00562 AC XY: 761AN XY: 135296
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GnomAD4 exome AF: 0.00294 AC: 4292AN: 1460942Hom.: 193 Cov.: 31 AF XY: 0.00252 AC XY: 1831AN XY: 726866
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GnomAD4 genome AF: 0.0275 AC: 4194AN: 152330Hom.: 203 Cov.: 32 AF XY: 0.0261 AC XY: 1944AN XY: 74494
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 26, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at