rs17036205

Positions:

• chr12-104697896-G-A

Variant summary

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

The NM_018413.6(CHST11):​c.205-59053G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0398 in 152,192 control chromosomes in the GnomAD database, including 256 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 0.040 (256 hom., cov: 31)
• Consequence: CHST11 NM_018413.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHST11	NM_018413.6	c.205-59053G>A		intron_variant		ENST00000303694.6
CHST11	NM_001173982.2	c.190-59053G>A		intron_variant
CHST11	XM_047428914.1	c.-33-59053G>A		intron_variant
CHST11	XM_047428915.1	c.-33-59053G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHST11	ENST00000303694.6	c.205-59053G>A		intron_variant		1	NM_018413.6	P4
CHST11	ENST00000549260.5	c.190-59053G>A		intron_variant		1		A1
CHST11	ENST00000549016.1	c.85-59053G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0399 AC: 6063 AN: 152074 Hom.: 255 Cov.: 31

Gnomad AFR AF: 0.0361

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0132

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.0891

Gnomad FIN AF: 0.0445

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0299

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0398 AC: 6060 AN: 152192 Hom.: 256 Cov.: 31 AF XY: 0.0425 AC XY: 3163 AN XY: 74380

Gnomad4 AFR AF: 0.0360

Gnomad4 AMR AF: 0.0131

Gnomad4 ASJ AF: 0.0135

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.0890

Gnomad4 FIN AF: 0.0445

Gnomad4 NFE AF: 0.0299

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0301 Hom.: 107

Bravo AF: 0.0386

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.49

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: rs17036205; hg19: chr12-105091674;