chr10-43157204-T-C

Variant names:

• chr10-43157204-T-C
• rs7921281
• NM_018590.5:c.661+1394T>C

Variant summary

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

The NM_018590.5(CSGALNACT2):​c.661+1394T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 151,656 control chromosomes in the GnomAD database, including 2,536 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 0.17 (2536 hom., cov: 32)
• Consequence: CSGALNACT2 NM_018590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.912
• Publications: 4 publications found

Genes affected

CSGALNACT2 (HGNC:24292): (chondroitin sulfate N-acetylgalactosaminyltransferase 2) This gene encodes a member of the chondroitin N-acetylgalactosaminyltransferase family. The encoded protein is involved in elongation during chondroitin sulfate synthesis. Alternative splicing of this gene results in multiple transcript variants. Two related pseudogenes have been identified on chromosome X. [provided by RefSeq, Feb 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018590.5. 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
	CSGALNACT2	NM_018590.5	MANE Select	c.661+1394T>C		intron	N/A	NP_061060.3
	CSGALNACT2	NM_001319654.1		c.661+1394T>C		intron	N/A	NP_001306583.1
	CSGALNACT2	NM_001319656.1		c.661+1394T>C		intron	N/A	NP_001306585.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSGALNACT2	ENST00000374466.4	TSL:1 MANE Select	c.661+1394T>C		intron	N/A	ENSP00000363590.3

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26428 AN: 151536 Hom.: 2535 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.174 AC: 26437 AN: 151656 Hom.: 2536 Cov.: 32 AF XY: 0.178 AC XY: 13164 AN XY: 74126

African (AFR) AF: 0.111 AC: 4605 AN: 41458

American (AMR) AF: 0.250 AC: 3804 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 703 AN: 3458

East Asian (EAS) AF: 0.112 AC: 578 AN: 5178

South Asian (SAS) AF: 0.243 AC: 1150 AN: 4732

European-Finnish (FIN) AF: 0.233 AC: 2451 AN: 10530

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12538 AN: 67754

Other (OTH) AF: 0.182 AC: 382 AN: 2102

Alfa AF: 0.197 Hom.: 1083

Bravo AF: 0.174

Asia WGS AF: 0.172 AC: 595 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	16
DANN	Benign	0.86
PhyloP100		0.91
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: rs7921281; hg19: chr10-43652652;