rs138804520

Variant names:

• chrX-46574585-C-T
• rs138804520
• NM_019886.4:c.654C>T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Moderate BP6_Moderate BP7 BS2

The NM_019886.4(CHST7):​c.654C>T​(p.Gly218Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0005 in 1,202,894 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 202 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.00099 (0 hom., 36 hem., cov: 24)
  • Exomes 𝑓: 0.00045 (0 hom. 166 hem.)
• Consequence: CHST7 NM_019886.4 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.471
• Publications: 1 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: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BP6: Variant X-46574585-C-T is Benign according to our data. Variant chrX-46574585-C-T is described in ClinVar as Benign. ClinVar VariationId is 722997.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.471 with no splicing effect.
• BS2: High Hemizygotes in GnomAd4 at 36 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019886.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHST7	NM_019886.4	MANE Select	c.654C>T	p.Gly218Gly	synonymous	Exon 1 of 2	NP_063939.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHST7	ENST00000276055.4	TSL:1 MANE Select	c.654C>T	p.Gly218Gly	synonymous	Exon 1 of 2	ENSP00000276055.3	Q9NS84
	CHST7	ENST00000868793.1		c.654C>T	p.Gly218Gly	synonymous	Exon 1 of 2	ENSP00000538852.1
	CHST7	ENST00000868794.1		c.654C>T	p.Gly218Gly	synonymous	Exon 1 of 2	ENSP00000538853.1

Frequencies

GnomAD3 genomes AF: 0.000991 AC: 112 AN: 113042 Hom.: 0 Cov.: 24

Gnomad AFR AF: 0.00196

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00193

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00422

Gnomad NFE AF: 0.000432

Gnomad OTH AF: 0.00392

GnomAD2 exomes AF: 0.000717 AC: 115 AN: 160285 AF XY: 0.000746

Gnomad AFR exome AF: 0.00308

Gnomad AMR exome AF: 0.00165

Gnomad ASJ exome AF: 0.000143

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000346

Gnomad OTH exome AF: 0.00297

GnomAD4 exome AF: 0.000450 AC: 490 AN: 1089798 Hom.: 0 Cov.: 32 AF XY: 0.000465 AC XY: 166 AN XY: 356930

African (AFR) AF: 0.00229 AC: 60 AN: 26250

American (AMR) AF: 0.00194 AC: 67 AN: 34510

Ashkenazi Jewish (ASJ) AF: 0.0000522 AC: 1 AN: 19168

East Asian (EAS) AF: 0.00 AC: 0 AN: 29814

South Asian (SAS) AF: 0.000113 AC: 6 AN: 53074

European-Finnish (FIN) AF: 0.0000509 AC: 2 AN: 39272

Middle Eastern (MID) AF: 0.00317 AC: 13 AN: 4103

European-Non Finnish (NFE) AF: 0.000343 AC: 287 AN: 837926

Other (OTH) AF: 0.00118 AC: 54 AN: 45681

GnomAD4 genome AF: 0.000990 AC: 112 AN: 113096 Hom.: 0 Cov.: 24 AF XY: 0.00102 AC XY: 36 AN XY: 35262

African (AFR) AF: 0.00195 AC: 61 AN: 31237

American (AMR) AF: 0.00193 AC: 21 AN: 10883

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2650

East Asian (EAS) AF: 0.00 AC: 0 AN: 3534

South Asian (SAS) AF: 0.00 AC: 0 AN: 2793

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6290

Middle Eastern (MID) AF: 0.00463 AC: 1 AN: 216

European-Non Finnish (NFE) AF: 0.000432 AC: 23 AN: 53270

Other (OTH) AF: 0.00387 AC: 6 AN: 1549

Alfa AF: 0.000434 Hom.: 2

Bravo AF: 0.00123

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	11
DANN	Benign	0.97
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs138804520; hg19: chrX-46434020; COSMIC: COSV52100162;