rs7921281

Positions:

• chr10-43157204-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSGALNACT2	NM_018590.5	c.661+1394T>C		intron_variant		ENST00000374466.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSGALNACT2	ENST00000374466.4	c.661+1394T>C		intron_variant		1	NM_018590.5	P1

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

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.182

Alfa AF: 0.202 Hom.: 1010

Bravo AF: 0.174

Asia WGS AF: 0.172 AC: 595 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	16
DANN	Benign	0.86

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: rs7921281; hg19: chr10-43652652;