X-46574585-C-T

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

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.471
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CHST7NM_019886.4 linkc.654C>T p.Gly218Gly synonymous_variant Exon 1 of 2 ENST00000276055.4 NP_063939.2 Q9NS84

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CHST7ENST00000276055.4 linkc.654C>T p.Gly218Gly synonymous_variant Exon 1 of 2 1 NM_019886.4 ENSP00000276055.3 Q9NS84

Frequencies

GnomAD3 genomes
AF:
0.000991
AC:
112
AN:
113042
Hom.:
0
Cov.:
24
AF XY:
0.00102
AC XY:
36
AN XY:
35198
show subpopulations
Gnomad AFR
AF:
0.00196
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00193
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00422
Gnomad NFE
AF:
0.000432
Gnomad OTH
AF:
0.00392
GnomAD3 exomes
AF:
0.000717
AC:
115
AN:
160285
Hom.:
0
AF XY:
0.000746
AC XY:
39
AN XY:
52271
show subpopulations
Gnomad AFR exome
AF:
0.00308
Gnomad AMR exome
AF:
0.00165
Gnomad ASJ exome
AF:
0.000143
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000579
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000346
Gnomad OTH exome
AF:
0.00297
GnomAD4 exome
AF:
0.000450
AC:
490
AN:
1089798
Hom.:
0
Cov.:
32
AF XY:
0.000465
AC XY:
166
AN XY:
356930
show subpopulations
Gnomad4 AFR exome
AF:
0.00229
Gnomad4 AMR exome
AF:
0.00194
Gnomad4 ASJ exome
AF:
0.0000522
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000113
Gnomad4 FIN exome
AF:
0.0000509
Gnomad4 NFE exome
AF:
0.000343
Gnomad4 OTH exome
AF:
0.00118
GnomAD4 genome
AF:
0.000990
AC:
112
AN:
113096
Hom.:
0
Cov.:
24
AF XY:
0.00102
AC XY:
36
AN XY:
35262
show subpopulations
Gnomad4 AFR
AF:
0.00195
Gnomad4 AMR
AF:
0.00193
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000432
Gnomad4 OTH
AF:
0.00387
Alfa
AF:
0.000434
Hom.:
2
Bravo
AF:
0.00123

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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.44
CADD
Benign
11
DANN
Benign
0.97

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs138804520; hg19: chrX-46434020; COSMIC: COSV52100162; API