12-104517468-T-C

Variant summary

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

The NM_018413.6(CHST11):c.118+59939T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,072 control chromosomes in the GnomAD database, including 6,255 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 0.28 (6255 hom., cov: 31)
• Consequence: CHST11 NM_018413.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHST11	NM_018413.6	c.118+59939T>C		intron_variant		ENST00000303694.6
CHST11	NM_001173982.2	c.103+59954T>C		intron_variant
CHST11	XM_047428914.1	c.-34+59939T>C		intron_variant
CHST11	XM_047428915.1	c.-34+59954T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHST11	ENST00000303694.6	c.118+59939T>C		intron_variant		1	NM_018413.6	P4
CHST11	ENST00000549260.5	c.103+59954T>C		intron_variant		1		A1
CHST11	ENST00000546689.1	c.103+59954T>C		intron_variant		2
CHST11	ENST00000547956.1	c.118+59939T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42180 AN: 151954 Hom.: 6240 Cov.: 31

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.278 AC: 42238 AN: 152072 Hom.: 6255 Cov.: 31 AF XY: 0.272 AC XY: 20189 AN XY: 74354

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.285

Alfa AF: 0.253 Hom.: 8711

Bravo AF: 0.302

Asia WGS AF: 0.265 AC: 920 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.45
Dann	Benign	0.60

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: rs1795849; hg19: chr12-104911246;