rs111686948
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001190880.3(HYI):c.505+5G>T variant causes a splice donor 5th base, intron change. The variant allele was found at a frequency of 0.00000124 in 1,612,424 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001190880.3 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SZT2 | NM_001365999.1 | c.*1450C>A | 3_prime_UTR_variant | 72/72 | ENST00000634258.3 | ||
HYI | NM_001190880.3 | c.505+5G>T | splice_donor_5th_base_variant, intron_variant | ENST00000372430.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SZT2 | ENST00000634258.3 | c.*1450C>A | 3_prime_UTR_variant | 72/72 | 5 | NM_001365999.1 | P1 | ||
HYI | ENST00000372430.9 | c.505+5G>T | splice_donor_5th_base_variant, intron_variant | 1 | NM_001190880.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152088Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460336Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 726214
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74274
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at