rs61734023

Variant names:

• chrX-46574889-G-C
• rs61734023
• NM_019886.4:c.958G>C

Your query was ambiguous. Multiple possible variants found:

• chrX-46574889-G-C
• chrX-46574889-G-A

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The NM_019886.4(CHST7):​c.958G>C​(p.Val320Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000569 in 1,159,447 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.00034 (0 hom., 7 hem., cov: 24)
  • Exomes 𝑓: 0.000027 (0 hom. 7 hem.)
• Consequence: CHST7 NM_019886.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.545
• Publications: 0 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 -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.119083256).
• BS2: High Hemizygotes in GnomAd4 at 7 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.958G>C	p.Val320Leu	missense	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.958G>C	p.Val320Leu	missense	Exon 1 of 2	ENSP00000276055.3	Q9NS84
	CHST7	ENST00000868793.1		c.958G>C	p.Val320Leu	missense	Exon 1 of 2	ENSP00000538852.1
	CHST7	ENST00000868794.1		c.958G>C	p.Val320Leu	missense	Exon 1 of 2	ENSP00000538853.1

Frequencies

GnomAD3 genomes AF: 0.000338 AC: 38 AN: 112585 Hom.: 0 Cov.: 24

Gnomad AFR AF: 0.00119

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000188

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000631 AC: 6 AN: 95114 AF XY: 0.0000378

Gnomad AFR exome AF: 0.000945

Gnomad AMR exome AF: 0.0000531

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000267 AC: 28 AN: 1046862 Hom.: 0 Cov.: 31 AF XY: 0.0000208 AC XY: 7 AN XY: 336398

African (AFR) AF: 0.000842 AC: 21 AN: 24943

American (AMR) AF: 0.000107 AC: 3 AN: 28161

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18066

East Asian (EAS) AF: 0.00 AC: 0 AN: 27492

South Asian (SAS) AF: 0.00 AC: 0 AN: 49010

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31218

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3913

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 819789

Other (OTH) AF: 0.0000904 AC: 4 AN: 44270

GnomAD4 genome AF: 0.000338 AC: 38 AN: 112585 Hom.: 0 Cov.: 24 AF XY: 0.000201 AC XY: 7 AN XY: 34803

African (AFR) AF: 0.00119 AC: 37 AN: 31096

American (AMR) AF: 0.00 AC: 0 AN: 10852

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2651

East Asian (EAS) AF: 0.00 AC: 0 AN: 3509

South Asian (SAS) AF: 0.00 AC: 0 AN: 2802

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6156

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 237

European-Non Finnish (NFE) AF: 0.0000188 AC: 1 AN: 53074

Other (OTH) AF: 0.00 AC: 0 AN: 1528

Alfa AF: 0.000427 Hom.: 0

Bravo AF: 0.000559

ExAC AF: 0.0000596 AC: 6

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.086
BayesDel_addAF	Benign	-0.33	T
BayesDel_noAF	Benign	-0.30
CADD	Benign	15
DANN	Uncertain	0.99
DEOGEN2	Benign	0.23	T
FATHMM_MKL	Benign	0.056	N
LIST_S2	Benign	0.53	T
M_CAP	Pathogenic	0.89	D
MetaRNN	Benign	0.12	T
MetaSVM	Uncertain	-0.16	T
MutationAssessor	Benign	0.11	N
PhyloP100		0.55
PrimateAI	Pathogenic	0.90	D
PROVEAN	Benign	-0.20	N
REVEL	Benign	0.21
Sift	Benign	0.19	T
Sift4G	Benign	0.36	T
Polyphen		0.067	B
Vest4		0.047
MutPred		0.47		Loss of MoRF binding (P = 0.0977)
MVP		0.88
ClinPred		0.011	T
GERP RS		3.2
Varity_R		0.11
gMVP		0.41
Mutation Taster		=98/2	polymorphism

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: rs61734023; hg19: chrX-46434324;