chr18-26990703-T-G

Variant names:

• chr18-26990703-T-G
• rs1436904
• NM_031422.6:c.202+33413A>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.202+33413A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,082 control chromosomes in the GnomAD database, including 9,977 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 0.35 (9977 hom., cov: 32)
• Consequence: CHST9 NM_031422.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• Publications: 72 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)

LOC124904275 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.452 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHST9	NM_031422.6	MANE Select	c.202+33413A>C		intron	N/A	NP_113610.2
	CHST9	NM_001398493.1		c.202+33413A>C		intron	N/A	NP_001385422.1
	CHST9	NM_001256316.2		c.202+33413A>C		intron	N/A	NP_001243245.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHST9	ENST00000618847.5	TSL:1 MANE Select	c.202+33413A>C		intron	N/A	ENSP00000480991.1
	CHST9	ENST00000581714.5	TSL:1	c.202+33413A>C		intron	N/A	ENSP00000462852.1
	AQP4-AS1	ENST00000578701.5	TSL:1	n.140+65858T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53506 AN: 151964 Hom.: 9980 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.352 AC: 53524 AN: 152082 Hom.: 9977 Cov.: 32 AF XY: 0.348 AC XY: 25860 AN XY: 74338

African (AFR) AF: 0.249 AC: 10334 AN: 41486

American (AMR) AF: 0.429 AC: 6555 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1161 AN: 3470

East Asian (EAS) AF: 0.468 AC: 2417 AN: 5170

South Asian (SAS) AF: 0.266 AC: 1279 AN: 4814

European-Finnish (FIN) AF: 0.325 AC: 3439 AN: 10570

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27133 AN: 67986

Other (OTH) AF: 0.372 AC: 786 AN: 2112

Alfa AF: 0.386 Hom.: 38667

Bravo AF: 0.359

Asia WGS AF: 0.398 AC: 1382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		-0.093
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: rs1436904; hg19: chr18-24570667;