22-50221052-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_020461.4(TUBGCP6):c.3307C>T(p.Arg1103Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00149 in 1,612,410 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1103Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_020461.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBGCP6 | NM_020461.4 | c.3307C>T | p.Arg1103Trp | missense_variant | 16/25 | ENST00000248846.10 | |
TUBGCP6 | XR_001755343.3 | n.3871C>T | non_coding_transcript_exon_variant | 16/20 | |||
TUBGCP6 | XR_938347.3 | n.3871C>T | non_coding_transcript_exon_variant | 16/23 | |||
TUBGCP6 | XR_007067982.1 | n.3048+976C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBGCP6 | ENST00000248846.10 | c.3307C>T | p.Arg1103Trp | missense_variant | 16/25 | 1 | NM_020461.4 | P1 | |
TUBGCP6 | ENST00000439308.6 | c.3307C>T | p.Arg1103Trp | missense_variant | 16/25 | 1 | |||
TUBGCP6 | ENST00000498611.5 | n.3617+223C>T | intron_variant, non_coding_transcript_variant | 1 | |||||
TUBGCP6 | ENST00000491449.5 | n.1614C>T | non_coding_transcript_exon_variant | 8/16 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00776 AC: 1175AN: 151352Hom.: 15 Cov.: 34
GnomAD3 exomes AF: 0.00191 AC: 481AN: 251452Hom.: 5 AF XY: 0.00129 AC XY: 175AN XY: 135908
GnomAD4 exome AF: 0.000840 AC: 1227AN: 1460942Hom.: 14 Cov.: 37 AF XY: 0.000722 AC XY: 525AN XY: 726806
GnomAD4 genome AF: 0.00777 AC: 1177AN: 151468Hom.: 15 Cov.: 34 AF XY: 0.00771 AC XY: 571AN XY: 74020
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 12, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Apr 19, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at