rs10778338

chr12-104500624-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018413.6(CHST11):c.118+43095A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,156 control chromosomes in the GnomAD database, including 3,061 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 0.19 (3061 hom., cov: 32)
• Consequence: CHST11 NM_018413.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567

Genes affected

CHST11 (HGNC:17422): (carbohydrate sulfotransferase 11) The protein encoded by this gene belongs to the sulfotransferase 2 family. It is localized to the golgi membrane, and catalyzes the transfer of sulfate to position 4 of the N-acetylgalactosamine (GalNAc) residue of chondroitin. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage, and is distributed on the surfaces of many cells and extracellular matrices. A chromosomal translocation involving this gene and IgH, t(12;14)(q23;q32), has been reported in a patient with B-cell chronic lymphocytic leukemia. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHST11	NM_018413.6	c.118+43095A>G		intron_variant		ENST00000303694.6
CHST11	NM_001173982.2	c.103+43110A>G		intron_variant
CHST11	XM_047428914.1	c.-34+43095A>G		intron_variant
CHST11	XM_047428915.1	c.-34+43110A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHST11	ENST00000303694.6	c.118+43095A>G		intron_variant		1	NM_018413.6	P4
CHST11	ENST00000549260.5	c.103+43110A>G		intron_variant		1		A1
CHST11	ENST00000546689.1	c.103+43110A>G		intron_variant		2
CHST11	ENST00000547956.1	c.118+43095A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29200 AN: 152038 Hom.: 3062 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0846

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.184

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.192 AC: 29220 AN: 152156 Hom.: 3061 Cov.: 32 AF XY: 0.186 AC XY: 13813 AN XY: 74394

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0846

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.182

Alfa AF: 0.183 Hom.: 5413

Bravo AF: 0.207

Asia WGS AF: 0.220 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.9
Dann	Benign	0.78

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

Other links and lift over

dbSNP: rs10778338; hg19: chr12-104894402;