15-101177490-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_014918.5(CHSY1):c.2307G>A(p.Ser769Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,613,296 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 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
CHSY1
NM_014918.5 synonymous
NM_014918.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.30
Publications
0 publications found
Genes affected
CHSY1 (HGNC:17198): (chondroitin sulfate synthase 1) This gene encodes a member of the chondroitin N-acetylgalactosaminyltransferase family. These enzymes possess dual glucuronyltransferase and galactosaminyltransferase activity and play critical roles in the biosynthesis of chondroitin sulfate, a glycosaminoglycan involved in many biological processes including cell proliferation and morphogenesis. Decreased expression of this gene may play a role in colorectal cancer, and mutations in this gene are a cause of temtamy preaxial brachydactyly syndrome. [provided by RefSeq, Dec 2011]
CHSY1 Gene-Disease associations (from GenCC):
- temtamy preaxial brachydactyly syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 15-101177490-C-T is Benign according to our data. Variant chr15-101177490-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2857244.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.3 with no splicing effect.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHSY1 | ENST00000254190.4 | c.2307G>A | p.Ser769Ser | synonymous_variant | Exon 3 of 3 | 1 | NM_014918.5 | ENSP00000254190.3 | ||
CHSY1 | ENST00000543813.2 | n.*1622G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 | ENSP00000496160.1 | ||||
CHSY1 | ENST00000543813.2 | n.*1622G>A | 3_prime_UTR_variant | Exon 3 of 3 | 2 | ENSP00000496160.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152130Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
152130
Hom.:
Cov.:
33
Gnomad AFR
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GnomAD2 exomes AF: 0.0000279 AC: 7AN: 251174 AF XY: 0.0000295 show subpopulations
GnomAD2 exomes
AF:
AC:
7
AN:
251174
AF XY:
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GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461048Hom.: 0 Cov.: 67 AF XY: 0.0000206 AC XY: 15AN XY: 726640 show subpopulations
GnomAD4 exome
AF:
AC:
34
AN:
1461048
Hom.:
Cov.:
67
AF XY:
AC XY:
15
AN XY:
726640
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33460
American (AMR)
AF:
AC:
7
AN:
44706
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26114
East Asian (EAS)
AF:
AC:
0
AN:
39672
South Asian (SAS)
AF:
AC:
2
AN:
86214
European-Finnish (FIN)
AF:
AC:
0
AN:
53416
Middle Eastern (MID)
AF:
AC:
0
AN:
5760
European-Non Finnish (NFE)
AF:
AC:
23
AN:
1111336
Other (OTH)
AF:
AC:
1
AN:
60370
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.451
Heterozygous variant carriers
0
2
4
5
7
9
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74438 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
152248
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
74438
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41530
American (AMR)
AF:
AC:
0
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5194
South Asian (SAS)
AF:
AC:
1
AN:
4820
European-Finnish (FIN)
AF:
AC:
0
AN:
10606
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
1
AN:
68024
Other (OTH)
AF:
AC:
0
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.550
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
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EpiControl
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Temtamy preaxial brachydactyly syndrome Benign:1
Nov 20, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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