rs760697

Variant names:

• chrX-46587909-G-A
• rs760697
• NM_019886.4:c.*32-9851G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_019886.4(CHST7):​c.*32-9851G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.56 (12585 hom., 18254 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: CHST7 NM_019886.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992
• Publications: 2 publications found

Genes affected

CHST7 (HGNC:13817): (carbohydrate sulfotransferase 7) This gene is a member of the Gal/GalNAc/GlcNAc (galactose/N-acetylgalactosamine/N-acetylglucosamine) 6-O-sulfotransferase (GST) family. Members of this family encode enzymes that catalyze the specific addition of sulfate groups to distinct hydroxyl and amino groups of carbohydrates. The encoded protein catalyzes the sulfation of 6-hydroxyl group of GalNAc in chondroitin. [provided by RefSeq, Aug 2013]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHST7	NM_019886.4	c.*32-9851G>A		intron_variant	Intron 1 of 1	ENST00000276055.4	NP_063939.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHST7	ENST00000276055.4	c.*32-9851G>A		intron_variant	Intron 1 of 1	1	NM_019886.4	ENSP00000276055.3

Frequencies

GnomAD3 genomes AF: 0.562 AC: 62017 AN: 110297 Hom.: 12591 Cov.: 22

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.578

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.562 AC: 62027 AN: 110349 Hom.: 12585 Cov.: 22 AF XY: 0.560 AC XY: 18254 AN XY: 32621

African (AFR) AF: 0.646 AC: 19619 AN: 30374

American (AMR) AF: 0.561 AC: 5785 AN: 10317

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1499 AN: 2630

East Asian (EAS) AF: 0.733 AC: 2531 AN: 3455

South Asian (SAS) AF: 0.647 AC: 1674 AN: 2588

European-Finnish (FIN) AF: 0.508 AC: 2962 AN: 5833

Middle Eastern (MID) AF: 0.675 AC: 143 AN: 212

European-Non Finnish (NFE) AF: 0.503 AC: 26559 AN: 52766

Other (OTH) AF: 0.581 AC: 876 AN: 1508

Alfa AF: 0.542 Hom.: 43626

Bravo AF: 0.574

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.048
DANN	Benign	0.74
PhyloP100		-0.99
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs760697; hg19: chrX-46447344;