rs6952809

Variant names:

• chr7-2408858-T-C
• rs6952809
• NM_018641.5:c.-78+5185T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018641.5(CHST12):​c.-78+5185T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 151,978 control chromosomes in the GnomAD database, including 32,344 homozygotes. 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 0.65 (32344 hom., cov: 31)
• Consequence: CHST12 NM_018641.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 24 publications found

Genes affected

CHST12 (HGNC:17423): (carbohydrate sulfotransferase 12) 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 the N-acetylgalactosamine (GalNAc) residue of chondroitin and desulfated dermatan sulfate. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage, and is distributed on the surfaces of many cells and extracellular matrices. Alternatively spliced transcript variants differing only in their 5' UTRs have been found for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHST12	NM_018641.5	c.-78+5185T>C		intron_variant	Intron 1 of 1	ENST00000618655.2	NP_061111.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHST12	ENST00000618655.2	c.-78+5185T>C		intron_variant	Intron 1 of 1	1	NM_018641.5	ENSP00000481912.1
CHST12	ENST00000258711.7	c.-78+5213T>C		intron_variant	Intron 1 of 1	1		ENSP00000258711.6
CHST12	ENST00000432336.1	c.-78+4652T>C		intron_variant	Intron 1 of 1	2		ENSP00000411207.1

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98668 AN: 151860 Hom.: 32315 Cov.: 31

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.650 AC: 98741 AN: 151978 Hom.: 32344 Cov.: 31 AF XY: 0.651 AC XY: 48323 AN XY: 74278

African (AFR) AF: 0.567 AC: 23479 AN: 41400

American (AMR) AF: 0.672 AC: 10250 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2421 AN: 3470

East Asian (EAS) AF: 0.802 AC: 4152 AN: 5178

South Asian (SAS) AF: 0.655 AC: 3159 AN: 4824

European-Finnish (FIN) AF: 0.646 AC: 6825 AN: 10566

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.682 AC: 46350 AN: 67974

Other (OTH) AF: 0.668 AC: 1410 AN: 2112

Alfa AF: 0.674 Hom.: 109902

Bravo AF: 0.651

Asia WGS AF: 0.660 AC: 2292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.31
DANN	Benign	0.49
PhyloP100		-1.1
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: rs6952809; hg19: chr7-2448493;