NM_020461.4:c.4223C>T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_020461.4(TUBGCP6):c.4223C>T(p.Ala1408Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0014 in 1,613,782 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TUBGCP6 | NM_020461.4 | c.4223C>T | p.Ala1408Val | missense_variant | Exon 18 of 25 | ENST00000248846.10 | NP_065194.3 | |
TUBGCP6 | XR_001755343.3 | n.4846C>T | non_coding_transcript_exon_variant | Exon 18 of 20 | ||||
TUBGCP6 | XR_007067982.1 | n.3163C>T | non_coding_transcript_exon_variant | Exon 17 of 19 | ||||
TUBGCP6 | XR_938347.3 | n.4787C>T | non_coding_transcript_exon_variant | Exon 18 of 23 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00197 AC: 300AN: 152224Hom.: 4 Cov.: 34
GnomAD3 exomes AF: 0.00294 AC: 737AN: 250858Hom.: 9 AF XY: 0.00242 AC XY: 328AN XY: 135690
GnomAD4 exome AF: 0.00135 AC: 1966AN: 1461440Hom.: 35 Cov.: 76 AF XY: 0.00126 AC XY: 917AN XY: 727052
GnomAD4 genome AF: 0.00198 AC: 301AN: 152342Hom.: 4 Cov.: 34 AF XY: 0.00217 AC XY: 162AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at