Variant 8-19405930-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001354483.2(CSGALNACT1):c.1449C>T(p.Asp483=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0657 in 1,614,034 control chromosomes in the GnomAD database, including 3,765 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.056 ( 269 hom., cov: 31)

Exomes 𝑓: 0.067 ( 3496 hom. )

Consequence

CSGALNACT1
NM_001354483.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.71

Variant links:

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]

CSGALNACT1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 8-19405930-G-A is Benign according to our data. Variant chr8-19405930-G-A is described in ClinVar as [Benign]. Clinvar id is 1275470.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.71 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSGALNACT1	NM_001354483.2 linkuse as main transcript	c.1449C>T	p.Asp483=	synonymous_variant	9/9	ENST00000692225.2	NP_001341412.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSGALNACT1	ENST00000692225.2 linkuse as main transcript	c.1449C>T	p.Asp483=	synonymous_variant	9/9		NM_001354483.2	ENSP00000509853	P1	Q8TDX6-1

Frequencies

GnomAD3 genomes

AF:

0.0556

AC:

8451

AN:

152040

Hom.:

271

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0287

Gnomad AMI

AF:

0.0691

Gnomad AMR

AF:

0.0508

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.0145

Gnomad SAS

AF:

0.0693

Gnomad FIN

AF:

0.0523

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.0720

Gnomad OTH

AF:

0.0664

GnomAD3 exomes

AF:

0.0616

AC:

15497

AN:

251432

Hom.:

556

AF XY:

0.0639

AC XY:

8677

AN XY:

135878

show subpopulations

Gnomad AFR exome

AF:

0.0263

Gnomad AMR exome

AF:

0.0392

Gnomad ASJ exome

AF:

0.114

Gnomad EAS exome

AF:

0.0166

Gnomad SAS exome

AF:

0.0760

Gnomad FIN exome

AF:

0.0593

Gnomad NFE exome

AF:

0.0722

Gnomad OTH exome

AF:

0.0724

GnomAD4 exome

AF:

0.0668

AC:

97644

AN:

1461876

Hom.:

3496

Cov.:

AF XY:

0.0673

AC XY:

48976

AN XY:

727238

show subpopulations

Gnomad4 AFR exome

AF:

0.0278

Gnomad4 AMR exome

AF:

0.0409

Gnomad4 ASJ exome

AF:

0.114

Gnomad4 EAS exome

AF:

0.0163

Gnomad4 SAS exome

AF:

0.0729

Gnomad4 FIN exome

AF:

0.0631

Gnomad4 NFE exome

AF:

0.0691

Gnomad4 OTH exome

AF:

0.0690

GnomAD4 genome

AF:

0.0555

AC:

8452

AN:

152158

Hom.:

269

Cov.:

AF XY:

0.0546

AC XY:

4061

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.0286

Gnomad4 AMR

AF:

0.0508

Gnomad4 ASJ

AF:

0.112

Gnomad4 EAS

AF:

0.0145

Gnomad4 SAS

AF:

0.0692

Gnomad4 FIN

AF:

0.0523

Gnomad4 NFE

AF:

0.0720

Gnomad4 OTH

AF:

0.0657

Alfa

AF:

0.0586

Hom.:

163

Bravo

AF:

0.0543

Asia WGS

AF:

0.0510

AC:

179

AN:

3478

EpiCase

AF:

0.0753

EpiControl

AF:

0.0768

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 09, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.24

DANN

Benign

0.50

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over