X-46574585-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_019886.4(CHST7):c.654C>T(p.Gly218Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0005 in 1,202,894 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 202 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00099 ( 0 hom., 36 hem., cov: 24)
Exomes 𝑓: 0.00045 ( 0 hom. 166 hem. )
Consequence
CHST7
NM_019886.4 synonymous
NM_019886.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.471
Genes affected
CHST7 (HGNC:13817): (carbohydrate sulfotransferase 7) This gene is a member of the Gal/GalNAc/GlcNAc (galactose/N-acetylgalactosamine/N-acetylglucosamine) 6-O-sulfotransferase (GST) family. Members of this family encode enzymes that catalyze the specific addition of sulfate groups to distinct hydroxyl and amino groups of carbohydrates. The encoded protein catalyzes the sulfation of 6-hydroxyl group of GalNAc in chondroitin. [provided by RefSeq, Aug 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant X-46574585-C-T is Benign according to our data. Variant chrX-46574585-C-T is described in ClinVar as [Benign]. Clinvar id is 722997.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.471 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 36 gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000991 AC: 112AN: 113042Hom.: 0 Cov.: 24 AF XY: 0.00102 AC XY: 36AN XY: 35198
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GnomAD3 exomes AF: 0.000717 AC: 115AN: 160285Hom.: 0 AF XY: 0.000746 AC XY: 39AN XY: 52271
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GnomAD4 exome AF: 0.000450 AC: 490AN: 1089798Hom.: 0 Cov.: 32 AF XY: 0.000465 AC XY: 166AN XY: 356930
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GnomAD4 genome AF: 0.000990 AC: 112AN: 113096Hom.: 0 Cov.: 24 AF XY: 0.00102 AC XY: 36AN XY: 35262
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
May 25, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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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