rs7092548

Variant names:

• chr10-43175357-C-T
• rs7092548
• NM_018590.5:c.1255-594C>T

Variant summary

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

The NM_018590.5(CSGALNACT2):​c.1255-594C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,156 control chromosomes in the GnomAD database, including 2,692 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 0.18 (2692 hom., cov: 32)
• Consequence: CSGALNACT2 NM_018590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSGALNACT2	NM_018590.5	c.1255-594C>T		intron_variant	Intron 6 of 7	ENST00000374466.4	NP_061060.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSGALNACT2	ENST00000374466.4	c.1255-594C>T		intron_variant	Intron 6 of 7	1	NM_018590.5	ENSP00000363590.3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27542 AN: 152038 Hom.: 2692 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.181 AC: 27554 AN: 152156 Hom.: 2692 Cov.: 32 AF XY: 0.184 AC XY: 13674 AN XY: 74378

African (AFR) AF: 0.141 AC: 5875 AN: 41534

American (AMR) AF: 0.248 AC: 3786 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 702 AN: 3466

East Asian (EAS) AF: 0.111 AC: 577 AN: 5176

South Asian (SAS) AF: 0.239 AC: 1153 AN: 4830

European-Finnish (FIN) AF: 0.231 AC: 2435 AN: 10562

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

European-Non Finnish (NFE) AF: 0.183 AC: 12417 AN: 67990

Other (OTH) AF: 0.182 AC: 383 AN: 2108

Alfa AF: 0.196 Hom.: 2102

Bravo AF: 0.183

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	-0.90
CADD	Benign	0.13
DANN	Benign	0.75
PhyloP100		-1.7
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: rs7092548; hg19: chr10-43670805;