10-43150406-C-T

Variant names:

• chr10-43150406-C-T
• rs2505506
• NM_018590.5:c.-253-4491C>T

Variant summary

Our verdict is Benign. Variant got -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

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSGALNACT2	NM_018590.5	c.-253-4491C>T		intron_variant	Intron 1 of 7	ENST00000374466.4	NP_061060.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSGALNACT2	ENST00000374466.4	c.-253-4491C>T		intron_variant	Intron 1 of 7	1	NM_018590.5	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

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.820

Alfa AF: 0.785 Hom.: 6742

Bravo AF: 0.836

Asia WGS AF: 0.625 AC: 2161 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.29

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: rs2505506; hg19: chr10-43645854;