Genetic Variant CHST11:c.-7C>A (chr12-104457405-C-A) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2

The NM_018413.6(CHST11):c.-7C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00484 in 1,609,418 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0028 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0051 ( 33 hom. )

Consequence

CHST11
NM_018413.6 5_prime_UTR

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 3.34

Variant links:

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]

CHST11 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.28).

BP6

Variant 12-104457405-C-A is Benign according to our data. Variant chr12-104457405-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 3044683.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAdExome4 at 33 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CHST11	NM_018413.6 link	c.-7C>A	5_prime_UTR_variant	Exon 1 of 3	ENST00000303694.6	NP_060883.1	Q9NPF2-1A0A024RBL0
CHST11	NM_001173982.2 link	c.-7C>A	5_prime_UTR_variant	Exon 1 of 3		NP_001167453.1	Q9NPF2-2
CHST11	XM_047428914.1 link	c.-158C>A	5_prime_UTR_variant	Exon 1 of 2		XP_047284870.1
CHST11	XM_047428915.1 link	c.-143C>A	5_prime_UTR_variant	Exon 1 of 2		XP_047284871.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CHST11	ENST00000303694 link	c.-7C>A	5_prime_UTR_variant	Exon 1 of 3	1	NM_018413.6	ENSP00000305725.5	Q9NPF2-1
CHST11	ENST00000549260 link	c.-7C>A	5_prime_UTR_variant	Exon 1 of 3	1		ENSP00000450004.1	Q9NPF2-2
CHST11	ENST00000547956 link	c.-7C>A	5_prime_UTR_variant	Exon 1 of 2	2		ENSP00000449093.1	F8VXK7
CHST11	ENST00000546689 link	c.-7C>A	5_prime_UTR_variant	Exon 1 of 2	2		ENSP00000448678.1	F8VRG6

Frequencies

GnomAD3 genomes

AF:

0.00282

AC:

429

AN:

152210

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00118

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.000589

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00535

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00238

AC:

595

AN:

249862

Hom.:

AF XY:

0.00246

AC XY:

333

AN XY:

135224

show subpopulations

Gnomad AFR exome

AF:

0.000929

Gnomad AMR exome

AF:

0.00119

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0000464

Gnomad NFE exome

AF:

0.00461

Gnomad OTH exome

AF:

0.00310

GnomAD4 exome

AF:

0.00505

AC:

7365

AN:

1457092

Hom.:

Cov.:

AF XY:

0.00483

AC XY:

3504

AN XY:

725214

show subpopulations

Gnomad4 AFR exome

AF:

0.00111

Gnomad4 AMR exome

AF:

0.00123

Gnomad4 ASJ exome

AF:

0.000153

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000232

Gnomad4 FIN exome

AF:

0.0000375

Gnomad4 NFE exome

AF:

0.00627

Gnomad4 OTH exome

AF:

0.00520

GnomAD4 genome

AF:

0.00282

AC:

429

AN:

152326

Hom.:

Cov.:

AF XY:

0.00246

AC XY:

183

AN XY:

74508

show subpopulations

Gnomad4 AFR

AF:

0.00118

Gnomad4 AMR

AF:

0.000588

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0000941

Gnomad4 NFE

AF:

0.00535

Gnomad4 OTH

AF:

0.00190

Alfa

AF:

0.00426

Hom.:

Bravo

AF:

0.00288

EpiCase

AF:

0.00496

EpiControl

AF:

0.00487

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CHST11-related disorder

Benign:1

Feb 19, 2024

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.28

CADD

Benign

DANN

Benign

0.94

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over