10-43157312-T-G

Position:

• chr10-43157312-T-G

Variant summary

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

The ENST00000374466.4(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 ENST00000374466.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841

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=-0.66).
• 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/exons	MANE	Protein	UniProt
CSGALNACT2	NM_018590.5	c.662-1403T>G		intron_variant		ENST00000374466.4	NP_061060.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSGALNACT2	ENST00000374466.4	c.662-1403T>G		intron_variant		1	NM_018590.5	ENSP00000363590	P1

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

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.181

Alfa AF: 0.209 Hom.: 834

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

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: rs7893332; hg19: chr10-43652760;