dbSNP rs2463437: CHST11:c.*2506G>A (chr12-104760309-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.910

Publications

11 publications found

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 Gene-Disease associations (from GenCC):

osteochondrodysplasia, brachydactyly, and overlapping malformed digits
Inheritance: AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

CHST11 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank	MANE	Protein
CHST11	NM_018413.6 link	c.*2506G>A	3_prime_UTR_variant	Exon 3 of 3	ENST00000303694.6	NP_060883.1
CHST11	NM_001173982.2 link	c.*2506G>A	3_prime_UTR_variant	Exon 3 of 3		NP_001167453.1
CHST11	XM_047428914.1 link	c.*2506G>A	3_prime_UTR_variant	Exon 2 of 2		XP_047284870.1
CHST11	XM_047428915.1 link	c.*2506G>A	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 link	c.*2506G>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_018413.6	ENSP00000305725.5
CHST11	ENST00000549260.5 link	c.*2506G>A		3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000450004.1

Frequencies

GnomAD3 genomes

AF:

0.653

AC:

98869

AN:

151496

Hom.:

32439

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AC:

AN:

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.652

AC:

98928

AN:

151614

Hom.:

32458

Cov.:

AF XY:

0.649

AC XY:

48026

AN XY:

74008

show subpopulations

African (AFR)

AF:

0.632

AC:

26066

AN:

41264

American (AMR)

AF:

0.655

AC:

9983

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.737

AC:

2559

AN:

3472

East Asian (EAS)

AF:

0.556

AC:

2870

AN:

5160

South Asian (SAS)

AF:

0.502

AC:

2407

AN:

4796

European-Finnish (FIN)

AF:

0.651

AC:

6813

AN:

10466

Middle Eastern (MID)

AF:

0.741

AC:

218

AN:

294

European-Non Finnish (NFE)

AF:

0.677

AC:

45957

AN:

67900

Other (OTH)

AF:

0.703

AC:

1479

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1679

3359

5038

6718

8397

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

798

1596

2394

3192

3990

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.672

Hom.:

73047

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

(source)

DANN

Benign

0.57

PhyloP100

0.91

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over