rs776400082
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020461.4(TUBGCP6):āc.407A>Gā(p.Asn136Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,613,910 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N136D) has been classified as Uncertain significance.
Frequency
Consequence
NM_020461.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBGCP6 | NM_020461.4 | c.407A>G | p.Asn136Ser | missense_variant | 1/25 | ENST00000248846.10 | |
TUBGCP6 | XR_001755343.3 | n.971A>G | non_coding_transcript_exon_variant | 1/20 | |||
TUBGCP6 | XR_007067982.1 | n.971A>G | non_coding_transcript_exon_variant | 1/19 | |||
TUBGCP6 | XR_938347.3 | n.971A>G | non_coding_transcript_exon_variant | 1/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBGCP6 | ENST00000248846.10 | c.407A>G | p.Asn136Ser | missense_variant | 1/25 | 1 | NM_020461.4 | P1 | |
TUBGCP6 | ENST00000439308.6 | c.407A>G | p.Asn136Ser | missense_variant | 1/25 | 1 | |||
TUBGCP6 | ENST00000498611.5 | n.940A>G | non_coding_transcript_exon_variant | 1/23 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251272Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135880
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461742Hom.: 0 Cov.: 32 AF XY: 0.0000481 AC XY: 35AN XY: 727154
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 19, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at