rs6508461

Variant names:

• chr18-26957690-G-C
• rs6508461
• NM_031422.6:c.203-13324C>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.203-13324C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 151,958 control chromosomes in the GnomAD database, including 2,785 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 0.13 (2785 hom., cov: 31)
• Consequence: CHST9 NM_031422.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.911
• Publications: 0 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHST9	NM_031422.6	MANE Select	c.203-13324C>G		intron	N/A	NP_113610.2	Q7L1S5-1
	CHST9	NM_001398493.1		c.203-13324C>G		intron	N/A	NP_001385422.1	Q7L1S5-1
	CHST9	NM_001256316.2		c.203-40340C>G		intron	N/A	NP_001243245.1	Q7L1S5-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHST9	ENST00000618847.5	TSL:1 MANE Select	c.203-13324C>G		intron	N/A	ENSP00000480991.1	Q7L1S5-1
	CHST9	ENST00000581714.5	TSL:1	c.203-13324C>G		intron	N/A	ENSP00000462852.1	Q7L1S5-1
	AQP4-AS1	ENST00000578701.5	TSL:1	n.140+32845G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19391 AN: 151840 Hom.: 2785 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0613

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0596

Gnomad FIN AF: 0.0386

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0357

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.128 AC: 19405 AN: 151958 Hom.: 2785 Cov.: 31 AF XY: 0.125 AC XY: 9275 AN XY: 74286

African (AFR) AF: 0.359 AC: 14846 AN: 41382

American (AMR) AF: 0.0611 AC: 934 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0484 AC: 168 AN: 3468

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5160

South Asian (SAS) AF: 0.0590 AC: 284 AN: 4812

European-Finnish (FIN) AF: 0.0386 AC: 407 AN: 10546

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0357 AC: 2426 AN: 67994

Other (OTH) AF: 0.103 AC: 218 AN: 2108

Alfa AF: 0.0905 Hom.: 226

Bravo AF: 0.139

Asia WGS AF: 0.0320 AC: 114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.41
DANN	Benign	0.40
PhyloP100		-0.91
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: rs6508461; hg19: chr18-24537654;