rs6952809

chr7-2408858-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CHST12	NM_018641.5	c.-78+5185T>C		intron_variant		ENST00000618655.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHST12	ENST00000618655.2	c.-78+5185T>C		intron_variant		1	NM_018641.5	P1
CHST12	ENST00000258711.7	c.-78+5213T>C		intron_variant		1		P1
CHST12	ENST00000432336.1	c.-78+4652T>C		intron_variant		2

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

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.668

Alfa AF: 0.678 Hom.: 46828

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

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: rs6952809; hg19: chr7-2448493;