NM_018590.5:c.662-1403T>G

Variant names:

• chr10-43157312-T-G
• rs7893332
• NM_018590.5:c.662-1403T>G

Variant summary

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

The NM_018590.5(CSGALNACT2):​c.662-1403T>G 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 152,140 control chromosomes in the GnomAD database, including 2,524 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 (2524 hom., cov: 31)
• Consequence: CSGALNACT2 NM_018590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841
• Publications: 7 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=-0.66).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSGALNACT2	NM_018590.5	c.662-1403T>G		intron_variant	Intron 2 of 7	ENST00000374466.4	NP_061060.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSGALNACT2	ENST00000374466.4	c.662-1403T>G		intron_variant	Intron 2 of 7	1	NM_018590.5	ENSP00000363590.3

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26408 AN: 152022 Hom.: 2524 Cov.: 31

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.174 AC: 26415 AN: 152140 Hom.: 2524 Cov.: 31 AF XY: 0.177 AC XY: 13149 AN XY: 74348

African (AFR) AF: 0.111 AC: 4607 AN: 41512

American (AMR) AF: 0.249 AC: 3802 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3466

East Asian (EAS) AF: 0.111 AC: 576 AN: 5168

South Asian (SAS) AF: 0.239 AC: 1152 AN: 4820

European-Finnish (FIN) AF: 0.230 AC: 2435 AN: 10570

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

European-Non Finnish (NFE) AF: 0.184 AC: 12535 AN: 67990

Other (OTH) AF: 0.181 AC: 382 AN: 2112

Alfa AF: 0.202 Hom.: 907

Bravo AF: 0.174

Asia WGS AF: 0.172 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	15
DANN	Benign	0.81
PhyloP100		0.84
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: rs7893332; hg19: chr10-43652760;