18-26906618-T-C

Position:

• chr18-26906618-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.*9641A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 152,004 control chromosomes in the GnomAD database, including 17,087 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 0.47 (17087 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CHST9 NM_031422.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

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:):

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 (SAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHST9	NM_031422.6	c.*9641A>G		3_prime_UTR_variant	6/6	ENST00000618847.5	NP_113610.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHST9	ENST00000618847	c.*9641A>G		3_prime_UTR_variant	6/6	1	NM_031422.6	ENSP00000480991.1

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71360 AN: 151884 Hom.: 17078 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.462

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.470 AC: 71406 AN: 152004 Hom.: 17087 Cov.: 32 AF XY: 0.477 AC XY: 35424 AN XY: 74288

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.465

Alfa AF: 0.428 Hom.: 8981

Bravo AF: 0.475

Asia WGS AF: 0.593 AC: 2060 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	2.1
DANN	Benign	0.68

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: rs151251; hg19: chr18-24486582;