rs9332435

Variant names:

• chr18-27173149-G-C
• rs9332435
• NM_031422.6:c.-97+11987C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031422.6(CHST9):​c.-97+11987C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 151,890 control chromosomes in the GnomAD database, including 39,420 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 0.72 (39420 hom., cov: 32)
• Consequence: CHST9 NM_031422.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390
• Publications: 1 publications found

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]

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHST9	NM_031422.6	c.-97+11987C>G		intron_variant	Intron 1 of 5	ENST00000618847.5	NP_113610.2
CHST9	NM_001256316.2	c.-97+11987C>G		intron_variant	Intron 1 of 4		NP_001243245.1
CHST9	XM_006722555.5	c.-97+11987C>G		intron_variant	Intron 1 of 5		XP_006722618.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHST9	ENST00000618847.5	c.-97+11987C>G		intron_variant	Intron 1 of 5	1	NM_031422.6	ENSP00000480991.1
AQP4-AS1	ENST00000578701.5	n.222-15594G>C		intron_variant	Intron 3 of 3	1
CHST9	ENST00000580774.2	c.-97+11987C>G		intron_variant	Intron 1 of 4	3		ENSP00000464655.1

Frequencies

GnomAD3 genomes AF: 0.718 AC: 108994 AN: 151772 Hom.: 39386 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.718 AC: 109079 AN: 151890 Hom.: 39420 Cov.: 32 AF XY: 0.711 AC XY: 52778 AN XY: 74246

African (AFR) AF: 0.769 AC: 31910 AN: 41474

American (AMR) AF: 0.678 AC: 10345 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2599 AN: 3466

East Asian (EAS) AF: 0.774 AC: 4014 AN: 5186

South Asian (SAS) AF: 0.622 AC: 2996 AN: 4818

European-Finnish (FIN) AF: 0.613 AC: 6454 AN: 10528

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48347 AN: 67852

Other (OTH) AF: 0.752 AC: 1584 AN: 2106

Alfa AF: 0.721 Hom.: 4926

Bravo AF: 0.722

Asia WGS AF: 0.700 AC: 2437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.40
PhyloP100		-0.39
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9332435; hg19: chr18-24753113;