rs6603859
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001114600.3(SZRD1):c.52-11795G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 152,006 control chromosomes in the GnomAD database, including 19,729 homozygotes. 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
Genomes: 𝑓 0.51 ( 19729 hom., cov: 32)
Consequence
SZRD1
NM_001114600.3 intron
NM_001114600.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0760
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SZRD1 | NM_001114600.3 | c.52-11795G>T | intron_variant | ENST00000401088.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SZRD1 | ENST00000401088.9 | c.52-11795G>T | intron_variant | 1 | NM_001114600.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.509 AC: 77353AN: 151888Hom.: 19715 Cov.: 32
GnomAD3 genomes
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151888
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.509 AC: 77409AN: 152006Hom.: 19729 Cov.: 32 AF XY: 0.508 AC XY: 37769AN XY: 74296
GnomAD4 genome
?
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77409
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152006
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32
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37769
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74296
Gnomad4 AFR
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Asia WGS
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1785
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at