chr7-71665590-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_022479.3(GALNT17):c.1260G>A(p.Pro420=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000263 in 1,612,380 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00028 ( 5 hom. )
Consequence
GALNT17
NM_022479.3 synonymous
NM_022479.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -8.94
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 7-71665590-G-A is Benign according to our data. Variant chr7-71665590-G-A is described in ClinVar as [Benign]. Clinvar id is 746087.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-8.94 with no splicing effect.
BS2
?
High Homozygotes in GnomAdExome at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALNT17 | NM_022479.3 | c.1260G>A | p.Pro420= | synonymous_variant | 7/11 | ENST00000333538.10 | |
GALNT17 | XM_011516467.4 | c.1260G>A | p.Pro420= | synonymous_variant | 7/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNT17 | ENST00000333538.10 | c.1260G>A | p.Pro420= | synonymous_variant | 7/11 | 1 | NM_022479.3 | P1 | |
GALNT17 | ENST00000467723.1 | n.1194G>A | non_coding_transcript_exon_variant | 7/11 | 2 | ||||
GALNT17 | ENST00000498380.6 | n.1662G>A | non_coding_transcript_exon_variant | 7/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152152Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000554 AC: 138AN: 249192Hom.: 2 AF XY: 0.000735 AC XY: 99AN XY: 134752
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GnomAD4 exome AF: 0.000275 AC: 402AN: 1460110Hom.: 5 Cov.: 31 AF XY: 0.000402 AC XY: 292AN XY: 726310
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 06, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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