rs371684007
Positions:
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS1
The NM_130468.4(CHST14):c.288G>A(p.Arg96=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000359 in 1,600,650 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0018 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00021 ( 1 hom. )
Consequence
CHST14
NM_130468.4 synonymous
NM_130468.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.67
Genes affected
CHST14 (HGNC:24464): (carbohydrate sulfotransferase 14) This gene encodes a member of the HNK-1 family of sulfotransferases. The encoded protein transfers sulfate to the C-4 hydroxyl of N-acetylgalactosamine residues in dermatan sulfate. Mutations in this gene have been associated with adducted thumb-clubfoot syndrome.[provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 15-40471501-G-A is Benign according to our data. Variant chr15-40471501-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 210731.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-1.67 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00179 (272/152288) while in subpopulation AFR AF= 0.00621 (258/41560). AF 95% confidence interval is 0.00559. There are 1 homozygotes in gnomad4. There are 130 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 |
---|---|---|---|---|---|---|---|
CHST14 | NM_130468.4 | c.288G>A | p.Arg96= | synonymous_variant | 1/1 | ENST00000306243.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHST14 | ENST00000306243.7 | c.288G>A | p.Arg96= | synonymous_variant | 1/1 | NM_130468.4 | P1 | ||
CHST14 | ENST00000559991.1 | c.288G>A | p.Arg96= | synonymous_variant | 1/2 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00178 AC: 271AN: 152168Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000526 AC: 122AN: 231776Hom.: 0 AF XY: 0.000415 AC XY: 53AN XY: 127796
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GnomAD4 exome AF: 0.000209 AC: 302AN: 1448362Hom.: 1 Cov.: 32 AF XY: 0.000169 AC XY: 122AN XY: 720008
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GnomAD4 genome ? AF: 0.00179 AC: 272AN: 152288Hom.: 1 Cov.: 32 AF XY: 0.00175 AC XY: 130AN XY: 74466
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 24, 2015 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 27, 2021 | - - |
Ehlers-Danlos syndrome, musculocontractural type Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 20, 2020 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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