Variant chr18-26916982-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_031422.6(CHST9):c.609A>G(p.Val203=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00312 in 1,613,922 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0028 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0032 ( 38 hom. )

Consequence

CHST9
NM_031422.6 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.624

Variant links:

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]

CHST9 links:

AQP4-AS1 (HGNC:26399): (AQP4 antisense RNA 1)

AQP4-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 18-26916982-T-C is Benign according to our data. Variant chr18-26916982-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2648627.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.624 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 38 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHST9	NM_031422.6 linkuse as main transcript	c.609A>G	p.Val203=	synonymous_variant	6/6	ENST00000618847.5	NP_113610.2
AQP4-AS1	NR_026908.1 linkuse as main transcript	n.176-7778T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHST9	ENST00000618847.5 linkuse as main transcript	c.609A>G	p.Val203=	synonymous_variant	6/6	1	NM_031422.6	ENSP00000480991	P1	Q7L1S5-1
AQP4-AS1	ENST00000578701.5 linkuse as main transcript	n.55-7778T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.00284

AC:

432

AN:

152124

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000314

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00433

Gnomad ASJ

AF:

0.0141

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00933

Gnomad FIN

AF:

0.00555

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00274

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.00443

AC:

1100

AN:

248318

Hom.:

AF XY:

0.00500

AC XY:

674

AN XY:

134696

show subpopulations

Gnomad AFR exome

AF:

0.000129

Gnomad AMR exome

AF:

0.00249

Gnomad ASJ exome

AF:

0.0192

Gnomad EAS exome

AF:

0.0000556

Gnomad SAS exome

AF:

0.0113

Gnomad FIN exome

AF:

0.00553

Gnomad NFE exome

AF:

0.00283

Gnomad OTH exome

AF:

0.00581

GnomAD4 exome

AF:

0.00315

AC:

4610

AN:

1461680

Hom.:

Cov.:

AF XY:

0.00349

AC XY:

2536

AN XY:

727140

show subpopulations

Gnomad4 AFR exome

AF:

0.000269

Gnomad4 AMR exome

AF:

0.00253

Gnomad4 ASJ exome

AF:

0.0180

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0101

Gnomad4 FIN exome

AF:

0.00517

Gnomad4 NFE exome

AF:

0.00232

Gnomad4 OTH exome

AF:

0.00431

GnomAD4 genome

AF:

0.00282

AC:

429

AN:

152242

Hom.:

Cov.:

AF XY:

0.00334

AC XY:

249

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.000313

Gnomad4 AMR

AF:

0.00432

Gnomad4 ASJ

AF:

0.0141

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00892

Gnomad4 FIN

AF:

0.00555

Gnomad4 NFE

AF:

0.00272

Gnomad4 OTH

AF:

0.00521

Alfa

AF:

0.00376

Hom.:

Bravo

AF:

0.00260

Asia WGS

AF:

0.00404

AC:

AN:

3478

EpiCase

AF:

0.00311

EpiControl

AF:

0.00350

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2022

CHST9: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

0.74

DANN

Benign

0.66

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over