rs2463437

Positions:

• chr12-104760309-G-A
• chr12-104760309-G-C
• chr12-104760309-G-T

Variant summary

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

The NM_018413.6(CHST11):​c.*2506G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 151,618 control chromosomes in the GnomAD database, including 32,460 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 0.65 (32458 hom., cov: 29)
  • Exomes 𝑓: 1.0 (2 hom.)
• Consequence: CHST11 NM_018413.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.910

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHST11	NM_018413.6	c.*2506G>A		3_prime_UTR_variant	3/3	ENST00000303694.6	NP_060883.1
CHST11	NM_001173982.2	c.*2506G>A		3_prime_UTR_variant	3/3		NP_001167453.1
CHST11	XM_047428914.1	c.*2506G>A		3_prime_UTR_variant	2/2		XP_047284870.1
CHST11	XM_047428915.1	c.*2506G>A		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.*2506G>A		3_prime_UTR_variant	3/3	1	NM_018413.6	ENSP00000305725	P4
CHST11	ENST00000549260.5	c.*2506G>A		3_prime_UTR_variant	3/3	1		ENSP00000450004	A1

Frequencies

GnomAD3 genomes AF: 0.653 AC: 98869 AN: 151496 Hom.: 32439 Cov.: 29

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.701

GnomAD4 exome AF: 1.00 AC: 4 AN: 4 Hom.: 2 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.652 AC: 98928 AN: 151614 Hom.: 32458 Cov.: 29 AF XY: 0.649 AC XY: 48026 AN XY: 74008

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.703

Alfa AF: 0.677 Hom.: 50348

Bravo AF: 0.657

Asia WGS AF: 0.545 AC: 1897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.5
DANN	Benign	0.57

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: rs2463437; hg19: chr12-105154087;