rs10227362

chr7-2417164-A-Gchr7-2417164-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018641.5(CHST12):c.-78+13491A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 151,934 control chromosomes in the GnomAD database, including 54,206 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 0.84 (54206 hom., cov: 29)
• Consequence: CHST12 NM_018641.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHST12	NM_018641.5	c.-78+13491A>G		intron_variant		ENST00000618655.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHST12	ENST00000618655.2	c.-78+13491A>G		intron_variant		1	NM_018641.5	P1
CHST12	ENST00000258711.7	c.-78+13519A>G		intron_variant		1		P1
CHST12	ENST00000432336.1	c.-78+12958A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.842 AC: 127829 AN: 151816 Hom.: 54155 Cov.: 29

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.842 AC: 127936 AN: 151934 Hom.: 54206 Cov.: 29 AF XY: 0.839 AC XY: 62280 AN XY: 74230

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.809

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.740

Gnomad4 NFE AF: 0.799

Gnomad4 OTH AF: 0.839

Alfa AF: 0.824 Hom.: 22331

Bravo AF: 0.858

Asia WGS AF: 0.843 AC: 2930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.0
Dann	Benign	0.24

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: rs10227362; hg19: chr7-2456799;