rs17143419
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022479.3(GALNT17):c.423-23643G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0956 in 152,176 control chromosomes in the GnomAD database, including 707 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 0.096 ( 707 hom., cov: 32)
Consequence
GALNT17
NM_022479.3 intron
NM_022479.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.169
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=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALNT17 | NM_022479.3 | c.423-23643G>T | intron_variant | ENST00000333538.10 | |||
GALNT17 | XM_011516467.4 | c.423-23643G>T | intron_variant | ||||
GALNT17 | XM_011516469.4 | c.423-23643G>T | intron_variant | ||||
GALNT17 | XM_017012521.3 | c.423-23643G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNT17 | ENST00000333538.10 | c.423-23643G>T | intron_variant | 1 | NM_022479.3 | P1 | |||
GALNT17 | ENST00000447516.5 | c.357-23643G>T | intron_variant | 4 | |||||
GALNT17 | ENST00000467723.1 | n.357-23643G>T | intron_variant, non_coding_transcript_variant | 2 | |||||
GALNT17 | ENST00000498380.6 | n.825-23643G>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0955 AC: 14527AN: 152058Hom.: 704 Cov.: 32
GnomAD3 genomes
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14527
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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: 0.0956 AC: 14548AN: 152176Hom.: 707 Cov.: 32 AF XY: 0.0934 AC XY: 6953AN XY: 74418
GnomAD4 genome
?
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14548
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152176
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32
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6953
AN XY:
74418
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206
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3476
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