chr1-43447923-G-GTGC
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_001365999.1(SZT2):c.9519_9521dupTGC(p.Ala3174dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000039 in 1,613,932 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001365999.1 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SZT2 | NM_001365999.1 | c.9519_9521dupTGC | p.Ala3174dup | disruptive_inframe_insertion | Exon 68 of 72 | ENST00000634258.3 | NP_001352928.1 | |
SZT2 | NM_015284.4 | c.9348_9350dupTGC | p.Ala3117dup | disruptive_inframe_insertion | Exon 67 of 71 | NP_056099.3 | ||
SZT2-AS1 | NR_046744.1 | n.549_551dupGCA | non_coding_transcript_exon_variant | Exon 2 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152050Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000636 AC: 16AN: 251416Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135886
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461882Hom.: 0 Cov.: 32 AF XY: 0.0000440 AC XY: 32AN XY: 727246
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152050Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74252
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant, c.9348_9350dup, results in the insertion of 1 amino acid(s) of the SZT2 protein (p.Ala3117dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs747931944, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with SZT2-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at