rs903247

Variant names:

• chr12-104759792-C-T
• rs903247
• NM_018413.6:c.*1989C>T

Variant summary

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

The NM_018413.6(CHST11):​c.*1989C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,920 control chromosomes in the GnomAD database, including 28,954 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 0.61 (28953 hom., cov: 31)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: CHST11 NM_018413.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHST11	NM_018413.6	c.*1989C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000303694.6	NP_060883.1
CHST11	NM_001173982.2	c.*1989C>T		3_prime_UTR_variant	Exon 3 of 3		NP_001167453.1
CHST11	XM_047428914.1	c.*1989C>T		3_prime_UTR_variant	Exon 2 of 2		XP_047284870.1
CHST11	XM_047428915.1	c.*1989C>T		3_prime_UTR_variant	Exon 2 of 2		XP_047284871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHST11	ENST00000303694.6	c.*1989C>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_018413.6	ENSP00000305725.5
CHST11	ENST00000549260.5	c.*1989C>T		3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000450004.1

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93001 AN: 151800 Hom.: 28934 Cov.: 31

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.659

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 FIN exome AF: 1.00

GnomAD4 genome AF: 0.613 AC: 93062 AN: 151918 Hom.: 28953 Cov.: 31 AF XY: 0.607 AC XY: 45033 AN XY: 74242

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.660

Alfa AF: 0.640 Hom.: 15837

Bravo AF: 0.616

Asia WGS AF: 0.460 AC: 1600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.2
DANN	Benign	0.84

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: rs903247; hg19: chr12-105153570;