rs11770998
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022479.3(GALNT17):c.239-88651A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0687 in 147,232 control chromosomes in the GnomAD database, including 449 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 0.069 ( 449 hom., cov: 29)
Consequence
GALNT17
NM_022479.3 intron
NM_022479.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.862
Genes affected
GALNT17 (HGNC:16347): (polypeptide N-acetylgalactosaminyltransferase 17) This gene encodes an N-acetylgalactosaminyltransferase. This gene is located centromeric to the common deleted region in Williams-Beuren syndrome (WBS), a multisystem developmental disorder caused by the deletion of contiguous genes at 7q11.23. This protein may play a role in membrane trafficking. [provided by RefSeq, Jan 2013]
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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=-0.93).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0871 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALNT17 | NM_022479.3 | c.239-88651A>G | intron_variant | ENST00000333538.10 | |||
GALNT17 | XM_011516467.4 | c.239-88651A>G | intron_variant | ||||
GALNT17 | XM_011516469.4 | c.239-88651A>G | intron_variant | ||||
GALNT17 | XM_017012521.3 | c.239-88651A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNT17 | ENST00000333538.10 | c.239-88651A>G | intron_variant | 1 | NM_022479.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0687 AC: 10118AN: 147180Hom.: 448 Cov.: 29
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0687 AC: 10115AN: 147232Hom.: 449 Cov.: 29 AF XY: 0.0705 AC XY: 5026AN XY: 71302
GnomAD4 genome
?
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195
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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