17-75522159-G-A
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_207346.3(TSEN54):c.1078G>A(p.Ala360Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000772 in 1,554,788 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A360V) has been classified as Likely benign.
Frequency
Consequence
NM_207346.3 missense
Scores
Clinical Significance
Conservation
Publications
- pontocerebellar hypoplasia type 2AInheritance: AR Classification: STRONG Submitted by: PanelApp Australia
- pontocerebellar hypoplasia type 4Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, PanelApp Australia
- pontocerebellar hypoplasia type 5Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- pontocerebellar hypoplasia type 2Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000120 AC: 2AN: 166470 AF XY: 0.0000112 show subpopulations
GnomAD4 exome AF: 0.00000784 AC: 11AN: 1402582Hom.: 0 Cov.: 72 AF XY: 0.00000868 AC XY: 6AN XY: 691504 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74368 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
ClinVar
Submissions by phenotype
not provided Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at