rs3840858
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The ENST00000701062.1(SNHG16):n.194+24858_194+24861dup variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0553 in 154,026 control chromosomes in the GnomAD database, including 265 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.055 ( 261 hom., cov: 31)
Exomes 𝑓: 0.067 ( 4 hom. )
Consequence
SNHG16
ENST00000701062.1 intron, non_coding_transcript
ENST00000701062.1 intron, non_coding_transcript
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.953
Genes affected
SNHG16 (HGNC:44352): (small nucleolar RNA host gene 16)
ST6GALNAC2 (HGNC:10867): (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 2) ST6GALNAC2 belongs to a family of sialyltransferases that add sialic acids to the nonreducing ends of glycoconjugates. At the cell surface, these modifications have roles in cell-cell and cell-substrate interactions, bacterial adhesion, and protein targeting (Samyn-Petit et al., 2000 [PubMed 10742600]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNHG16 | ENST00000701062.1 | n.194+24858_194+24861dup | intron_variant, non_coding_transcript_variant | ||||||
ST6GALNAC2 | ENST00000588005.5 | n.88+614_88+615insCCGG | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0551 AC: 8384AN: 152154Hom.: 257 Cov.: 31
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GnomAD4 exome AF: 0.0666 AC: 117AN: 1758Hom.: 4 AF XY: 0.0701 AC XY: 68AN XY: 970
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GnomAD4 genome AF: 0.0551 AC: 8397AN: 152268Hom.: 261 Cov.: 31 AF XY: 0.0546 AC XY: 4069AN XY: 74456
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at