18-26990703-T-G

Position:

• chr18-26990703-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHST9	NM_031422.6	c.202+33413A>C		intron_variant		ENST00000618847.5
LOC124904275	XR_007066323.1	n.77-7329T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHST9	ENST00000618847.5	c.202+33413A>C		intron_variant		1	NM_031422.6	P1
AQP4-AS1	ENST00000578701.5	n.140+65858T>G		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.372

Alfa AF: 0.390 Hom.: 17300

Bravo AF: 0.359

Asia WGS AF: 0.398 AC: 1382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.64

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: rs1436904; hg19: chr18-24570667;