NM_018413.6:c.205-59053G>A

Variant names:

• chr12-104697896-G-A
• rs17036205
• NM_018413.6:c.205-59053G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

CHST11 Gene-Disease associations (from GenCC):

• osteochondrodysplasia, brachydactyly, and overlapping malformed digits

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018413.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHST11	NM_018413.6	MANE Select	c.205-59053G>A		intron	N/A	NP_060883.1
	CHST11	NM_001173982.2		c.190-59053G>A		intron	N/A	NP_001167453.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHST11	ENST00000303694.6	TSL:1 MANE Select	c.205-59053G>A		intron	N/A	ENSP00000305725.5
	CHST11	ENST00000549260.5	TSL:1	c.190-59053G>A		intron	N/A	ENSP00000450004.1
	CHST11	ENST00000549016.1	TSL:4	c.85-59053G>A		intron	N/A	ENSP00000449095.1

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

African (AFR) AF: 0.0360 AC: 1496 AN: 41516

American (AMR) AF: 0.0131 AC: 201 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0135 AC: 47 AN: 3470

East Asian (EAS) AF: 0.249 AC: 1283 AN: 5154

South Asian (SAS) AF: 0.0890 AC: 428 AN: 4810

European-Finnish (FIN) AF: 0.0445 AC: 472 AN: 10612

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0299 AC: 2034 AN: 68024

Other (OTH) AF: 0.0341 AC: 72 AN: 2112

Alfa AF: 0.0334 Hom.: 379

Bravo AF: 0.0386

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.49
PhyloP100		0.49
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17036205; hg19: chr12-105091674;