rs760697

chrX-46587909-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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

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

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS2: High Homozygotes in GnomAd at 12591 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHST7	NM_019886.4	c.*32-9851G>A		intron_variant		ENST00000276055.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHST7	ENST00000276055.4	c.*32-9851G>A		intron_variant		1	NM_019886.4	P1

Frequencies

GnomAD3 genomes AF: 0.562 AC: 62017 AN: 110297 Hom.: 12591 Cov.: 22 AF XY: 0.560 AC XY: 18234 AN XY: 32559

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

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.581

Alfa AF: 0.523 Hom.: 25744

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

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: rs760697; hg19: chrX-46447344;