16-75473196-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_021615.5(CHST6):c.*5445G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 152,286 control chromosomes in the GnomAD database, including 33,746 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.66 ( 33720 hom., cov: 33)
Exomes 𝑓: 0.71 ( 26 hom. )
Consequence
CHST6
NM_021615.5 3_prime_UTR
NM_021615.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.100
Genes affected
CHST6 (HGNC:6938): (carbohydrate sulfotransferase 6) The protein encoded by this gene is an enzyme that catalyzes the transfer of a sulfate group to the GlcNAc residues of keratan. Keratan sulfate helps maintain corneal transparency. Defects in this gene are a cause of macular corneal dystrophy (MCD). [provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BP6
?
Variant 16-75473196-C-T is Benign according to our data. Variant chr16-75473196-C-T is described in ClinVar as [Benign]. Clinvar id is 320505.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHST6 | NM_021615.5 | c.*5445G>A | 3_prime_UTR_variant | 3/3 | ENST00000332272.9 | ||
CHST6 | NR_163480.1 | n.1005G>A | non_coding_transcript_exon_variant | 4/4 | |||
CHST6 | NR_163481.1 | n.849G>A | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHST6 | ENST00000332272.9 | c.*5445G>A | 3_prime_UTR_variant | 3/3 | 3 | NM_021615.5 | P1 | ||
CHST6 | ENST00000649824.1 | c.*870G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 |
Frequencies
GnomAD3 genomes ? AF: 0.664 AC: 100981AN: 152054Hom.: 33670 Cov.: 33
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GnomAD4 exome AF: 0.705 AC: 79AN: 112Hom.: 26 Cov.: 0 AF XY: 0.645 AC XY: 40AN XY: 62
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GnomAD4 genome ? AF: 0.664 AC: 101088AN: 152174Hom.: 33720 Cov.: 33 AF XY: 0.664 AC XY: 49433AN XY: 74398
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Macular corneal dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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Name
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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