Genetic Variant CHST9:c.*9641A>G (chr18-26906618-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_031422.6(CHST9):c.*9641A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 152,004 control chromosomes in the GnomAD database, including 17,087 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 0.47 ( 17087 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

CHST9
NM_031422.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.169

Publications

3 publications found

Variant links:

Genes affected

CHST9 (HGNC:19898): (carbohydrate sulfotransferase 9) 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 non-reducing N-acetylgalactosamine (GalNAc) residues in both N-glycans and O-glycans. Sulfate groups on carbohydrates confer highly specific functions to glycoproteins, glycolipids, and proteoglycans, and are critical for cell-cell interaction, signal transduction, and embryonic development. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Aug 2011]

CHST9 links:

AQP4-AS1 (HGNC:26399): (AQP4 antisense RNA 1)

AQP4-AS1 links:

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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=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031422.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CHST9	NM_031422.6	MANE Select	c.*9641A>G	3_prime_UTR	Exon 6 of 6	NP_113610.2
CHST9	NM_001398493.1		c.*9641A>G	3_prime_UTR	Exon 5 of 5	NP_001385422.1
CHST9	NM_001256316.2		c.*10710A>G	3_prime_UTR	Exon 5 of 5	NP_001243245.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CHST9	ENST00000618847.5	TSL:1 MANE Select	c.*9641A>G	3_prime_UTR	Exon 6 of 6	ENSP00000480991.1
AQP4-AS1	ENST00000578701.5	TSL:1	n.55-18142T>C	intron	N/A
AQP4-AS1	ENST00000568797.3	TSL:2	n.175+13626T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.470

AC:

71360

AN:

151884

Hom.:

17078

Cov.:

show subpopulations

Gnomad AFR

AF:

0.487

Gnomad AMI

AF:

0.534

Gnomad AMR

AF:

0.535

Gnomad ASJ

AF:

0.383

Gnomad EAS

AF:

0.538

Gnomad SAS

AF:

0.603

Gnomad FIN

AF:

0.474

Gnomad MID

AF:

0.548

Gnomad NFE

AF:

0.433

Gnomad OTH

AF:

0.462

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

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)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.470

AC:

71406

AN:

152004

Hom.:

17087

Cov.:

AF XY:

0.477

AC XY:

35424

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.487

AC:

20189

AN:

41452

American (AMR)

AF:

0.534

AC:

8154

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.383

AC:

1327

AN:

3464

East Asian (EAS)

AF:

0.538

AC:

2777

AN:

5166

South Asian (SAS)

AF:

0.601

AC:

2888

AN:

4806

European-Finnish (FIN)

AF:

0.474

AC:

5002

AN:

10550

Middle Eastern (MID)

AF:

0.538

AC:

156

AN:

290

European-Non Finnish (NFE)

AF:

0.433

AC:

29445

AN:

67986

Other (OTH)

AF:

0.465

AC:

982

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1935

3869

5804

7738

9673

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

660

1320

1980

2640

3300

<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:

0.443

Hom.:

19631

Bravo

AF:

0.475

Asia WGS

AF:

0.593

AC:

2060

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.1

(source)

DANN

Benign

0.68

PhyloP100

0.17

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over