chr4-25159110-TAA-T
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_016955.4(SEPSECS):c.115-5_115-4delTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000706 in 1,456,956 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_016955.4 splice_region, intron
Scores
Clinical Significance
Conservation
Publications
- pontocerebellar hypoplasia type 2DInheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Broad Center for Mendelian Genomics, PanelApp Australia, G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- pontocerebellar hypoplasia type 2Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- progressive cerebello-cerebral atrophyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000567 AC: 8AN: 141122Hom.: 0 Cov.: 26 show subpopulations
GnomAD2 exomes AF: 0.00104 AC: 133AN: 128440 AF XY: 0.00108 show subpopulations
GnomAD4 exome AF: 0.000775 AC: 1020AN: 1315834Hom.: 0 AF XY: 0.000784 AC XY: 513AN XY: 654306 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
Age Distribution
GnomAD4 genome AF: 0.0000567 AC: 8AN: 141122Hom.: 0 Cov.: 26 AF XY: 0.0000878 AC XY: 6AN XY: 68324 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
Age Distribution
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at