chr22-50217763-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_020461.4(TUBGCP6):c.5433C>T(p.Asn1811=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000304 in 1,614,082 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000027 ( 0 hom. )
Consequence
TUBGCP6
NM_020461.4 synonymous
NM_020461.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.10
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
Variant 22-50217763-G-A is Benign according to our data. Variant chr22-50217763-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1580188.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBGCP6 | NM_020461.4 | c.5433C>T | p.Asn1811= | synonymous_variant | 25/25 | ENST00000248846.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBGCP6 | ENST00000248846.10 | c.5433C>T | p.Asn1811= | synonymous_variant | 25/25 | 1 | NM_020461.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152172Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000104 AC: 26AN: 251110Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135804
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GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461792Hom.: 0 Cov.: 34 AF XY: 0.0000289 AC XY: 21AN XY: 727190
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GnomAD4 genome AF: 0.0000591 AC: 9AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74460
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 21, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at