16-75473444-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_021615.5(CHST6):c.*5197C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000204 in 152,302 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., cov: 32)
Consequence
CHST6
NM_021615.5 3_prime_UTR
NM_021615.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.103
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 -8 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
?
Variant 16-75473444-G-A is Benign according to our data. Variant chr16-75473444-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 887929.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000204 (31/152302) while in subpopulation AFR AF= 0.00065 (27/41570). AF 95% confidence interval is 0.000458. There are 0 homozygotes in gnomad4. There are 18 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHST6 | NM_021615.5 | c.*5197C>T | 3_prime_UTR_variant | 3/3 | ENST00000332272.9 | ||
CHST6 | NR_163480.1 | n.757C>T | non_coding_transcript_exon_variant | 4/4 | |||
CHST6 | NR_163481.1 | n.601C>T | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHST6 | ENST00000332272.9 | c.*5197C>T | 3_prime_UTR_variant | 3/3 | 3 | NM_021615.5 | P1 | ||
CHST6 | ENST00000649341.1 | c.*132C>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 | |||||
CHST6 | ENST00000649824.1 | c.*622C>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152184Hom.: 0 Cov.: 32
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GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74466
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Macular corneal dystrophy Benign:1
Likely 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Computational scores
Source:
Name
Calibrated prediction
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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