12-104758613-A-G

Variant names:

• chr12-104758613-A-G
• rs2468110
• NM_018413.6:c.*810A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018413.6(CHST11):​c.*810A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 152,030 control chromosomes in the GnomAD database, including 30,908 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 0.64 (30906 hom., cov: 31)
  • Exomes 𝑓: 0.67 (2 hom.)
• Consequence: CHST11 NM_018413.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.437
• Publications: 11 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: Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.664 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHST11	NM_018413.6	MANE Select	c.*810A>G		3_prime_UTR	Exon 3 of 3	NP_060883.1	Q9NPF2-1
	CHST11	NM_001173982.2		c.*810A>G		3_prime_UTR	Exon 3 of 3	NP_001167453.1	Q9NPF2-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHST11	ENST00000303694.6	TSL:1 MANE Select	c.*810A>G		3_prime_UTR	Exon 3 of 3	ENSP00000305725.5	Q9NPF2-1
	CHST11	ENST00000549260.5	TSL:1	c.*810A>G		3_prime_UTR	Exon 3 of 3	ENSP00000450004.1	Q9NPF2-2

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96488 AN: 151906 Hom.: 30882 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.686

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.635 AC: 96558 AN: 152024 Hom.: 30906 Cov.: 31 AF XY: 0.631 AC XY: 46903 AN XY: 74316

African (AFR) AF: 0.593 AC: 24564 AN: 41426

American (AMR) AF: 0.641 AC: 9800 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2548 AN: 3466

East Asian (EAS) AF: 0.533 AC: 2759 AN: 5172

South Asian (SAS) AF: 0.496 AC: 2395 AN: 4826

European-Finnish (FIN) AF: 0.639 AC: 6755 AN: 10570

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45496 AN: 67964

Other (OTH) AF: 0.686 AC: 1448 AN: 2112

Alfa AF: 0.648 Hom.: 29686

Bravo AF: 0.638

Asia WGS AF: 0.529 AC: 1841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.0
DANN	Benign	0.78
PhyloP100		0.44
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: rs2468110; hg19: chr12-105152391;