rs9953270

chr18-27107407-T-C

Variant summary

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

The NM_031422.6(CHST9):c.121+35282A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 152,072 control chromosomes in the GnomAD database, including 9,012 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 0.34 (9012 hom., cov: 32)
• Consequence: CHST9 NM_031422.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHST9	NM_031422.6	c.121+35282A>G		intron_variant		ENST00000618847.5
CHST9	NM_001256316.2	c.121+35282A>G		intron_variant
CHST9	NM_001398493.1	c.121+35282A>G		intron_variant
CHST9	XM_006722555.5	c.121+35282A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHST9	ENST00000618847.5	c.121+35282A>G		intron_variant		1	NM_031422.6	P1
CHST9	ENST00000581714.5	c.121+35282A>G		intron_variant		1		P1
AQP4-AS1	ENST00000578701.5	n.141-40291T>C		intron_variant, non_coding_transcript_variant		1
CHST9	ENST00000580774.2	c.121+35282A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51295 AN: 151954 Hom.: 9004 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.338 AC: 51335 AN: 152072 Hom.: 9012 Cov.: 32 AF XY: 0.337 AC XY: 25055 AN XY: 74358

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.357

Alfa AF: 0.331 Hom.: 8233

Bravo AF: 0.345

Asia WGS AF: 0.487 AC: 1694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.94
Dann	Benign	0.42

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: rs9953270; hg19: chr18-24687371;