20-5834428-A-T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152504.4(SHLD1):c.179-28596A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 152,026 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_152504.4 intron
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHLD1 | ENST00000303142.11 | c.179-28596A>T | intron_variant | Intron 2 of 2 | 1 | NM_152504.4 | ENSP00000305875.6 | |||
SHLD1 | ENST00000442185.1 | c.320-28596A>T | intron_variant | Intron 3 of 3 | 3 | ENSP00000410534.1 | ||||
SHLD1 | ENST00000445603.1 | c.179-28596A>T | intron_variant | Intron 3 of 3 | 3 | ENSP00000399331.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152026Hom.: 0 Cov.: 32 show subpopulations
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152026Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74248 show subpopulations
Age Distribution
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at