rs62341097
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_017423.3(GALNT7):c.126+4828G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0305 in 152,196 control chromosomes in the GnomAD database, including 91 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 0.031 ( 91 hom., cov: 32)
Consequence
GALNT7
NM_017423.3 intron
NM_017423.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.708
Genes affected
GALNT7 (HGNC:4129): (polypeptide N-acetylgalactosaminyltransferase 7) This gene encodes GalNAc transferase 7, a member of the GalNAc-transferase family. The enzyme encoded by this gene controls the initiation step of mucin-type O-linked protein glycosylation and transfer of N-acetylgalactosamine to serine and threonine amino acid residues. This enzyme is a type II transmembrane protein and shares common sequence motifs with other family members. Unlike other family members, this enzyme shows exclusive specificity for partially GalNAc-glycosylated acceptor substrates and shows no activity with non-glycosylated peptides. This protein may function as a follow-up enzyme in the initiation step of O-glycosylation. [provided by RefSeq, Jul 2008]
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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=-0.85).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0305 (4644/152196) while in subpopulation NFE AF= 0.0481 (3271/68020). AF 95% confidence interval is 0.0467. There are 91 homozygotes in gnomad4. There are 2155 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 91 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALNT7 | NM_017423.3 | c.126+4828G>A | intron_variant | ENST00000265000.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNT7 | ENST00000265000.9 | c.126+4828G>A | intron_variant | 1 | NM_017423.3 | P3 | |||
GALNT7 | ENST00000505308.6 | c.126+4828G>A | intron_variant | 2 | A1 | ||||
GALNT7 | ENST00000512285.5 | c.126+4828G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0306 AC: 4646AN: 152078Hom.: 91 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0305 AC: 4644AN: 152196Hom.: 91 Cov.: 32 AF XY: 0.0290 AC XY: 2155AN XY: 74400
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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