rs752974
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001318100.2(LZTS2):c.-40C>T variant causes a splice region, 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 1,492,776 control chromosomes in the GnomAD database, including 163,078 homozygotes. In-silico tool predicts a benign outcome for this variant. 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_001318100.2 splice_region, 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LZTS2 | NM_001318100.2 | c.-40C>T | splice_region_variant, 5_prime_UTR_variant | 2/5 | ENST00000454422.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LZTS2 | ENST00000454422.2 | c.-40C>T | splice_region_variant, 5_prime_UTR_variant | 2/5 | 2 | NM_001318100.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.383 AC: 58295AN: 152018Hom.: 13444 Cov.: 33
GnomAD3 exomes AF: 0.427 AC: 68891AN: 161208Hom.: 16665 AF XY: 0.436 AC XY: 37525AN XY: 86086
GnomAD4 exome AF: 0.463 AC: 620388AN: 1340640Hom.: 149627 Cov.: 33 AF XY: 0.462 AC XY: 302160AN XY: 654630
GnomAD4 genome ? AF: 0.383 AC: 58304AN: 152136Hom.: 13451 Cov.: 33 AF XY: 0.386 AC XY: 28707AN XY: 74398
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at