10-43150406-C-T

Variant names:

• chr10-43150406-C-T
• rs2505506
• NM_018590.5:c.-253-4491C>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.-253-4491C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 152,232 control chromosomes in the GnomAD database, including 53,028 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 0.83 (53028 hom., cov: 32)
• Consequence: CSGALNACT2 NM_018590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.669
• Publications: 8 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 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.-253-4491C>T		intron	N/A	NP_061060.3
	CSGALNACT2	NR_135077.2		n.124-4491C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSGALNACT2	ENST00000374466.4	TSL:1 MANE Select	c.-253-4491C>T		intron	N/A	ENSP00000363590.3

Frequencies

GnomAD3 genomes AF: 0.830 AC: 126278 AN: 152114 Hom.: 52963 Cov.: 32

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.830 AC: 126408 AN: 152232 Hom.: 53028 Cov.: 32 AF XY: 0.828 AC XY: 61597 AN XY: 74436

African (AFR) AF: 0.914 AC: 37964 AN: 41548

American (AMR) AF: 0.805 AC: 12321 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2652 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2602 AN: 5178

South Asian (SAS) AF: 0.711 AC: 3432 AN: 4826

European-Finnish (FIN) AF: 0.821 AC: 8693 AN: 10586

Middle Eastern (MID) AF: 0.791 AC: 231 AN: 292

European-Non Finnish (NFE) AF: 0.823 AC: 55941 AN: 68006

Other (OTH) AF: 0.820 AC: 1733 AN: 2114

Alfa AF: 0.801 Hom.: 8779

Bravo AF: 0.836

Asia WGS AF: 0.625 AC: 2161 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.29
PhyloP100		-0.67
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: rs2505506; hg19: chr10-43645854;