rs16943181

chr18-27013650-T-Achr18-27013650-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.202+10466A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,186 control chromosomes in the GnomAD database, including 3,299 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 0.14 (3299 hom., cov: 33)
• Consequence: CHST9 NM_031422.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHST9	NM_031422.6	c.202+10466A>T		intron_variant		ENST00000618847.5
CHST9	NM_001256316.2	c.202+10466A>T		intron_variant
CHST9	NM_001398493.1	c.202+10466A>T		intron_variant
CHST9	XM_006722555.5	c.202+10466A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHST9	ENST00000618847.5	c.202+10466A>T		intron_variant		1	NM_031422.6	P1
CHST9	ENST00000581714.5	c.202+10466A>T		intron_variant		1		P1
AQP4-AS1	ENST00000578701.5	n.140+88805T>A		intron_variant, non_coding_transcript_variant		1
CHST9	ENST00000580774.2	c.202+10466A>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20909 AN: 152068 Hom.: 3295 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0579

Gnomad FIN AF: 0.0384

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0357

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.138 AC: 20933 AN: 152186 Hom.: 3299 Cov.: 33 AF XY: 0.134 AC XY: 9944 AN XY: 74418

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.0649

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0571

Gnomad4 FIN AF: 0.0384

Gnomad4 NFE AF: 0.0358

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0312 Hom.: 61

Bravo AF: 0.150

Asia WGS AF: 0.0400 AC: 140 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.49
Dann	Benign	0.59

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: rs16943181; hg19: chr18-24593614;