chr12-104667230-C-T

Position:

• chr12-104667230-C-T

Variant summary

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

The NM_018413.6(CHST11):​c.204+65239C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,908 control chromosomes in the GnomAD database, including 13,571 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 0.41 (13571 hom., cov: 31)
• Consequence: CHST11 NM_018413.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHST11	NM_018413.6	c.204+65239C>T		intron_variant		ENST00000303694.6
CHST11	NM_001173982.2	c.189+65239C>T		intron_variant
CHST11	XM_047428914.1	c.-33-89719C>T		intron_variant
CHST11	XM_047428915.1	c.-33-89719C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHST11	ENST00000303694.6	c.204+65239C>T		intron_variant		1	NM_018413.6	P4
CHST11	ENST00000549260.5	c.189+65239C>T		intron_variant		1		A1
CHST11	ENST00000549016.1	c.84+65239C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62142 AN: 151790 Hom.: 13529 Cov.: 31

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.410 AC: 62242 AN: 151908 Hom.: 13571 Cov.: 31 AF XY: 0.406 AC XY: 30113 AN XY: 74234

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.414

Alfa AF: 0.386 Hom.: 2261

Bravo AF: 0.418

Asia WGS AF: 0.451 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.81
DANN	Benign	0.52

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: rs835488; hg19: chr12-105061008;