rs10502485

Variant names:

• chr18-27067723-A-G
• rs10502485
• NM_031422.6:c.122-19220T>C

Variant summary

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

The NM_031422.6(CHST9):​c.122-19220T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0555 in 152,190 control chromosomes in the GnomAD database, including 348 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 0.056 (348 hom., cov: 32)
• Consequence: CHST9 NM_031422.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHST9	NM_031422.6	c.122-19220T>C		intron_variant	Intron 2 of 5	ENST00000618847.5	NP_113610.2
CHST9	NM_001398493.1	c.122-19220T>C		intron_variant	Intron 1 of 4		NP_001385422.1
CHST9	NM_001256316.2	c.122-19220T>C		intron_variant	Intron 2 of 4		NP_001243245.1
CHST9	XM_006722555.5	c.122-19220T>C		intron_variant	Intron 2 of 5		XP_006722618.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHST9	ENST00000618847.5	c.122-19220T>C		intron_variant	Intron 2 of 5	1	NM_031422.6	ENSP00000480991.1
CHST9	ENST00000581714.5	c.122-19220T>C		intron_variant	Intron 1 of 4	1		ENSP00000462852.1
AQP4-AS1	ENST00000578701.5	n.141-79975A>G		intron_variant	Intron 2 of 3	1
CHST9	ENST00000580774.2	c.122-19220T>C		intron_variant	Intron 2 of 4	3		ENSP00000464655.1

Frequencies

GnomAD3 genomes AF: 0.0553 AC: 8414 AN: 152072 Hom.: 347 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0707

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.0912

Gnomad SAS AF: 0.0421

Gnomad FIN AF: 0.0184

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0268

Gnomad OTH AF: 0.0531

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

GnomAD4 genome AF: 0.0555 AC: 8448 AN: 152190 Hom.: 348 Cov.: 32 AF XY: 0.0550 AC XY: 4090 AN XY: 74414

African (AFR) AF: 0.109 AC: 4507 AN: 41526

American (AMR) AF: 0.0709 AC: 1083 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0124 AC: 43 AN: 3472

East Asian (EAS) AF: 0.0912 AC: 472 AN: 5176

South Asian (SAS) AF: 0.0417 AC: 201 AN: 4822

European-Finnish (FIN) AF: 0.0184 AC: 195 AN: 10614

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0268 AC: 1823 AN: 67994

Other (OTH) AF: 0.0520 AC: 110 AN: 2114

Alfa AF: 0.0385 Hom.: 303

Bravo AF: 0.0650

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.66
PhyloP100		-0.086
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: rs10502485; hg19: chr18-24647687;