rs1941114

Variant names:

• chr18-27034255-C-A
• NM_031422.6:c.161-10098G>T

Your query was ambiguous. Multiple possible variants found:

• chr18-27034255-C-A
• chr18-27034255-C-G
• chr18-27034255-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_031422.6(CHST9):​c.161-10098G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: CHST9 NM_031422.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHST9	NM_031422.6	c.161-10098G>T		intron_variant	Intron 3 of 5	ENST00000618847.5	NP_113610.2
CHST9	NM_001398493.1	c.161-10098G>T		intron_variant	Intron 2 of 4		NP_001385422.1
CHST9	NM_001256316.2	c.161-10098G>T		intron_variant	Intron 3 of 4		NP_001243245.1
CHST9	XM_006722555.5	c.161-10098G>T		intron_variant	Intron 3 of 5		XP_006722618.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHST9	ENST00000618847.5	c.161-10098G>T		intron_variant	Intron 3 of 5	1	NM_031422.6	ENSP00000480991.1
CHST9	ENST00000581714.5	c.161-10098G>T		intron_variant	Intron 2 of 4	1		ENSP00000462852.1
AQP4-AS1	ENST00000578701.5	n.140+109410C>A		intron_variant	Intron 2 of 3	1
CHST9	ENST00000580774.2	c.161-10098G>T		intron_variant	Intron 3 of 4	3		ENSP00000464655.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.99
DANN	Benign	0.69

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr18-24614219;