1-43389965-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001365999.1(SZT2):c.-4T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000998 in 1,423,298 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001365999.1 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000251 AC: 16AN: 63652Hom.: 0 AF XY: 0.000318 AC XY: 11AN XY: 34544
GnomAD4 exome AF: 0.0000975 AC: 124AN: 1271240Hom.: 0 Cov.: 34 AF XY: 0.000108 AC XY: 67AN XY: 618424
GnomAD4 genome AF: 0.000118 AC: 18AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74276
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.-4T>C variant is located in the 5' untranslated region (5’ UTR) of the SZT2 gene. This variant results from a T to C substitution 4 bases upstream from the first translated codon. Based on data from the NHLBI Exome Sequencing Project (ESP), the C allele has an overall frequency of approximately 0.01% (1/12392) total alleles studied and 0.01% (1/8210) European American alleles. This nucleotide position is highly conserved in available vertebrate species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is not predicted to have any significant effect on this splice acceptor site; however, direct evidence is unavailable. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at