12-104758613-A-G

Position:

• chr12-104758613-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.*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

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHST11	NM_018413.6	c.*810A>G		3_prime_UTR_variant	3/3	ENST00000303694.6	NP_060883.1
CHST11	NM_001173982.2	c.*810A>G		3_prime_UTR_variant	3/3		NP_001167453.1
CHST11	XM_047428914.1	c.*810A>G		3_prime_UTR_variant	2/2		XP_047284870.1
CHST11	XM_047428915.1	c.*810A>G		3_prime_UTR_variant	2/2		XP_047284871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHST11	ENST00000303694.6	c.*810A>G		3_prime_UTR_variant	3/3	1	NM_018413.6	ENSP00000305725.5
CHST11	ENST00000549260.5	c.*810A>G		3_prime_UTR_variant	3/3	1		ENSP00000450004.1

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

Gnomad4 NFE exome AF: 1.00

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

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.686

Alfa AF: 0.650 Hom.: 17796

Bravo AF: 0.638

Asia WGS AF: 0.529 AC: 1841 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	5.0
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: rs2468110; hg19: chr12-105152391;