Variant 10-43183348-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018590.5(CSGALNACT2):c.1435C>T(p.Pro479Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 1,613,590 control chromosomes in the GnomAD database, including 54,615 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.21 ( 3953 hom., cov: 32)

Exomes 𝑓: 0.26 ( 50662 hom. )

Consequence

CSGALNACT2
NM_018590.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.96

Variant links:

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]

CSGALNACT2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0014256835).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSGALNACT2	NM_018590.5 linkuse as main transcript	c.1435C>T	p.Pro479Ser	missense_variant	8/8	ENST00000374466.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSGALNACT2	ENST00000374466.4 linkuse as main transcript	c.1435C>T	p.Pro479Ser	missense_variant	8/8	1	NM_018590.5	P1	Q8N6G5-1

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

31637

AN:

151930

Hom.:

3943

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0666

Gnomad AMI

AF:

0.336

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.230

Gnomad EAS

AF:

0.229

Gnomad SAS

AF:

0.167

Gnomad FIN

AF:

0.324

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.274

Gnomad OTH

AF:

0.207

GnomAD3 exomes

AF:

0.232

AC:

58350

AN:

251466

Hom.:

7472

AF XY:

0.235

AC XY:

31975

AN XY:

135910

show subpopulations

Gnomad AFR exome

AF:

0.0632

Gnomad AMR exome

AF:

0.169

Gnomad ASJ exome

AF:

0.229

Gnomad EAS exome

AF:

0.232

Gnomad SAS exome

AF:

0.170

Gnomad FIN exome

AF:

0.319

Gnomad NFE exome

AF:

0.275

Gnomad OTH exome

AF:

0.237

GnomAD4 exome

AF:

0.258

AC:

377267

AN:

1461542

Hom.:

50662

Cov.:

AF XY:

0.256

AC XY:

186359

AN XY:

727090

show subpopulations

Gnomad4 AFR exome

AF:

0.0547

Gnomad4 AMR exome

AF:

0.173

Gnomad4 ASJ exome

AF:

0.226

Gnomad4 EAS exome

AF:

0.215

Gnomad4 SAS exome

AF:

0.173

Gnomad4 FIN exome

AF:

0.308

Gnomad4 NFE exome

AF:

0.275

Gnomad4 OTH exome

AF:

0.242

GnomAD4 genome

AF:

0.208

AC:

31662

AN:

152048

Hom.:

3953

Cov.:

AF XY:

0.212

AC XY:

15740

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.0665

Gnomad4 AMR

AF:

0.211

Gnomad4 ASJ

AF:

0.230

Gnomad4 EAS

AF:

0.229

Gnomad4 SAS

AF:

0.167

Gnomad4 FIN

AF:

0.324

Gnomad4 NFE

AF:

0.274

Gnomad4 OTH

AF:

0.213

Alfa

AF:

0.230

Hom.:

2179

Bravo

AF:

0.193

TwinsUK

AF:

0.270

AC:

1001

ALSPAC

AF:

0.272

AC:

1047

ESP6500AA

AF:

0.0695

AC:

306

ESP6500EA

AF:

0.267

AC:

2293

ExAC

AF:

0.232

AC:

28127

Asia WGS

AF:

0.189

AC:

656

AN:

3478

EpiCase

AF:

0.275

EpiControl

AF:

0.273

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.69

BayesDel_noAF

Benign

-0.63

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.098

Eigen

Benign

0.091

Eigen_PC

Uncertain

0.28

FATHMM_MKL

Uncertain

0.88

LIST_S2

Benign

0.74

MetaRNN

Benign

0.0014

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.91

MutationTaster

Benign

0.0000012

PrimateAI

Uncertain

0.54

PROVEAN

Uncertain

-2.8

REVEL

Benign

0.12

Sift

Benign

0.19

Sift4G

Benign

0.20

Polyphen

0.13

Vest4

0.034

MPC

0.23

ClinPred

0.026

GERP RS

5.9

Varity_R

0.12

gMVP

0.61

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over