NM_001270764.2:c.*1571G>A

Variant names:

• chr10-124008578-C-T
• rs12915
• NM_001270764.2:c.*1571G>A

Variant summary

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

The NM_001270764.2(CHST15):​c.*1571G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 1,012,358 control chromosomes in the GnomAD database, including 95,514 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 0.41 (12871 hom., cov: 32)
  • Exomes 𝑓: 0.44 (82643 hom.)
• Consequence: CHST15 NM_001270764.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 7 publications found

Genes affected

CHST15 (HGNC:18137): (carbohydrate sulfotransferase 15) Chondroitin sulfate (CS) is a glycosaminoglycan which is an important structural component of the extracellular matrix and which links to proteins to form proteoglycans. Chondroitin sulfate E (CS-E) is an isomer of chondroitin sulfate in which the C-4 and C-6 hydroxyl groups are sulfated. This gene encodes a type II transmembrane glycoprotein that acts as a sulfotransferase to transfer sulfate to the C-6 hydroxal group of chondroitin sulfate. This gene has also been identified as being co-expressed with RAG1 in B-cells and as potentially acting as a B-cell surface signaling receptor. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001270764.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHST15	NM_001270764.2	MANE Select	c.*1571G>A		3_prime_UTR	Exon 8 of 8	NP_001257693.1
	CHST15	NM_015892.5		c.*1571G>A		3_prime_UTR	Exon 8 of 8	NP_056976.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHST15	ENST00000435907.6	TSL:1 MANE Select	c.*1571G>A		3_prime_UTR	Exon 8 of 8	ENSP00000402394.1
	CHST15	ENST00000346248.7	TSL:1	c.*1571G>A		3_prime_UTR	Exon 8 of 8	ENSP00000333947.6
	CHST15	ENST00000874549.1		c.*1571G>A		3_prime_UTR	Exon 8 of 8	ENSP00000544608.1

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62109 AN: 151842 Hom.: 12874 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.391

GnomAD4 exome AF: 0.437 AC: 375976 AN: 860398 Hom.: 82643 Cov.: 35 AF XY: 0.438 AC XY: 174914 AN XY: 399660

African (AFR) AF: 0.328 AC: 5504 AN: 16800

American (AMR) AF: 0.360 AC: 1207 AN: 3356

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 2510 AN: 5716

East Asian (EAS) AF: 0.467 AC: 2486 AN: 5324

South Asian (SAS) AF: 0.383 AC: 7936 AN: 20720

European-Finnish (FIN) AF: 0.492 AC: 618 AN: 1256

Middle Eastern (MID) AF: 0.378 AC: 641 AN: 1694

European-Non Finnish (NFE) AF: 0.442 AC: 343113 AN: 777034

Other (OTH) AF: 0.420 AC: 11961 AN: 28498

GnomAD4 genome AF: 0.409 AC: 62126 AN: 151960 Hom.: 12871 Cov.: 32 AF XY: 0.410 AC XY: 30480 AN XY: 74266

African (AFR) AF: 0.338 AC: 14020 AN: 41438

American (AMR) AF: 0.364 AC: 5560 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1506 AN: 3468

East Asian (EAS) AF: 0.449 AC: 2313 AN: 5148

South Asian (SAS) AF: 0.400 AC: 1929 AN: 4824

European-Finnish (FIN) AF: 0.471 AC: 4973 AN: 10548

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30456 AN: 67946

Other (OTH) AF: 0.391 AC: 825 AN: 2110

Alfa AF: 0.427 Hom.: 6509

Bravo AF: 0.398

Asia WGS AF: 0.384 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.67
PhyloP100		-0.30
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
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: rs12915; hg19: chr10-125768094;