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GeneBe

rs244745

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_175856.5(CHSY3):c.1086+15107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,606 control chromosomes in the GnomAD database, including 9,375 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.35 ( 9375 hom., cov: 30)

Consequence

CHSY3
NM_175856.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.34
Variant links:
Genes affected
CHSY3 (HGNC:24293): (chondroitin sulfate synthase 3) CSS3 is a glycosyltransferase that has both glucuronyltransferase and N-acetylgalactosaminyltransferase activities (Yada et al., 2003 [PubMed 12907687]).[supplied by OMIM, Mar 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CHSY3NM_175856.5 linkuse as main transcriptc.1086+15107G>A intron_variant ENST00000305031.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CHSY3ENST00000305031.5 linkuse as main transcriptc.1086+15107G>A intron_variant 1 NM_175856.5 P1
CHSY3ENST00000507545.1 linkuse as main transcriptn.274+15107G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.349
AC:
52836
AN:
151488
Hom.:
9364
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.276
Gnomad AMI
AF:
0.313
Gnomad AMR
AF:
0.395
Gnomad ASJ
AF:
0.327
Gnomad EAS
AF:
0.419
Gnomad SAS
AF:
0.460
Gnomad FIN
AF:
0.449
Gnomad MID
AF:
0.345
Gnomad NFE
AF:
0.355
Gnomad OTH
AF:
0.354
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.349
AC:
52873
AN:
151606
Hom.:
9375
Cov.:
30
AF XY:
0.357
AC XY:
26439
AN XY:
74068
show subpopulations
Gnomad4 AFR
AF:
0.277
Gnomad4 AMR
AF:
0.394
Gnomad4 ASJ
AF:
0.327
Gnomad4 EAS
AF:
0.419
Gnomad4 SAS
AF:
0.460
Gnomad4 FIN
AF:
0.449
Gnomad4 NFE
AF:
0.355
Gnomad4 OTH
AF:
0.352
Alfa
AF:
0.351
Hom.:
1272
Bravo
AF:
0.339
Asia WGS
AF:
0.449
AC:
1560
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
Cadd
Benign
5.2
Dann
Benign
0.63

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs244745; hg19: chr5-129259160; COSMIC: COSV59274281; API