rs7816924

Positions:

• chr8-19682127-C-T

Variant summary

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

The NM_001354483.2(CSGALNACT1):​c.-392+75059G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 151,998 control chromosomes in the GnomAD database, including 3,268 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 0.19 (3268 hom., cov: 31)
• Consequence: CSGALNACT1 NM_001354483.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470

Genes affected

CSGALNACT1 (HGNC:24290): (chondroitin sulfate N-acetylgalactosaminyltransferase 1) This gene encodes an enzyme that transfers N-acetylglucosamine (GalNAc) to the core tetrasaccharide linker and to elongating chondroitin sulfate chains in proteoglycans. Knockout of the orthologous mouse gene indicates that the protein is necessary for normal cartilage development and aggrecan metabolism. Mutations in this gene are associated with multiple sclerosis progression, and with mild skeletal dysplasia and joint laxity. [provided by RefSeq, Aug 2017]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSGALNACT1	NM_001354483.2	c.-392+75059G>A		intron_variant		ENST00000692225.2
LOC124901899	XR_007060841.1	n.283+3300C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSGALNACT1	ENST00000692225.2	c.-392+75059G>A		intron_variant			NM_001354483.2	P1
	ENST00000519803.1	n.256+3300C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29451 AN: 151886 Hom.: 3247 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.0727

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.128

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.194 AC: 29500 AN: 151998 Hom.: 3268 Cov.: 31 AF XY: 0.193 AC XY: 14314 AN XY: 74284

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.0727

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.184

Alfa AF: 0.163 Hom.: 1072

Bravo AF: 0.206

Asia WGS AF: 0.307 AC: 1065 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.99
DANN	Benign	0.37

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7816924; hg19: chr8-19539638;