chr7-2418047-G-A

Variant names:

• chr7-2418047-G-A
• rs12534223
• NM_018641.5:c.-78+14374G>A

Variant summary

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

The NM_018641.5(CHST12):​c.-78+14374G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0877 in 152,342 control chromosomes in the GnomAD database, including 683 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 0.088 (683 hom., cov: 31)
• Consequence: CHST12 NM_018641.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHST12	NM_018641.5	c.-78+14374G>A		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+14374G>A		intron_variant	Intron 1 of 1	1	NM_018641.5	ENSP00000481912.1
CHST12	ENST00000258711.7	c.-78+14402G>A		intron_variant	Intron 1 of 1	1		ENSP00000258711.6
CHST12	ENST00000432336.1	c.-78+13841G>A		intron_variant	Intron 1 of 1	2		ENSP00000411207.1

Frequencies

GnomAD3 genomes AF: 0.0877 AC: 13357 AN: 152224 Hom.: 685 Cov.: 31

Gnomad AFR AF: 0.0291

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0898

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0860

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

GnomAD4 genome AF: 0.0877 AC: 13354 AN: 152342 Hom.: 683 Cov.: 31 AF XY: 0.0861 AC XY: 6412 AN XY: 74498

Gnomad4 AFR AF: 0.0290

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.0893

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.0817

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0860

Alfa AF: 0.0961 Hom.: 109

Bravo AF: 0.0871

Asia WGS AF: 0.129 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.46

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: rs12534223; hg19: chr7-2457682;