Variant rs3817602 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_001384711.1(GLT8D2):c.588C>T(p.Leu196=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0352 in 1,612,234 control chromosomes in the GnomAD database, including 2,854 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 0.082 ( 1015 hom., cov: 32)

Exomes 𝑓: 0.030 ( 1839 hom. )

Consequence

GLT8D2
NM_001384711.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.800

Variant links:

Genes affected

GLT8D2 (HGNC:24890): (glycosyltransferase 8 domain containing 2) Predicted to enable glycosyltransferase activity. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

GLT8D2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP7

Synonymous conserved (PhyloP=-0.8 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLT8D2	NM_001384711.1 linkuse as main transcript	c.588C>T	p.Leu196=	synonymous_variant	8/11	ENST00000360814.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
GLT8D2	ENST00000360814.9 linkuse as main transcript	c.588C>T	p.Leu196=	synonymous_variant	8/11	1	NM_001384711.1	P1
GLT8D2	ENST00000546436.5 linkuse as main transcript	c.588C>T	p.Leu196=	synonymous_variant	7/10	5		P1
GLT8D2	ENST00000548660.5 linkuse as main transcript	c.588C>T	p.Leu196=	synonymous_variant	8/11	2		P1
GLT8D2	ENST00000552572.1 linkuse as main transcript	n.100C>T		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes

AF:

0.0814

AC:

12385

AN:

152132

Hom.:

1009

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0736

Gnomad ASJ

AF:

0.0680

Gnomad EAS

AF:

0.148

Gnomad SAS

AF:

0.0263

Gnomad FIN

AF:

0.0191

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.0197

Gnomad OTH

AF:

0.0813

GnomAD3 exomes

AF:

0.0504

AC:

12645

AN:

250692

Hom.:

702

AF XY:

0.0457

AC XY:

6187

AN XY:

135496

show subpopulations

Gnomad AFR exome

AF:

0.206

Gnomad AMR exome

AF:

0.0590

Gnomad ASJ exome

AF:

0.0665

Gnomad EAS exome

AF:

0.149

Gnomad SAS exome

AF:

0.0248

Gnomad FIN exome

AF:

0.0208

Gnomad NFE exome

AF:

0.0209

Gnomad OTH exome

AF:

0.0477

GnomAD4 exome

AF:

0.0303

AC:

44281

AN:

1459984

Hom.:

1839

Cov.:

AF XY:

0.0300

AC XY:

21759

AN XY:

726344

show subpopulations

Gnomad4 AFR exome

AF:

0.208

Gnomad4 AMR exome

AF:

0.0587

Gnomad4 ASJ exome

AF:

0.0617

Gnomad4 EAS exome

AF:

0.169

Gnomad4 SAS exome

AF:

0.0256

Gnomad4 FIN exome

AF:

0.0192

Gnomad4 NFE exome

AF:

0.0180

Gnomad4 OTH exome

AF:

0.0452

GnomAD4 genome

AF:

0.0815

AC:

12410

AN:

152250

Hom.:

1015

Cov.:

AF XY:

0.0814

AC XY:

6065

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.202

Gnomad4 AMR

AF:

0.0734

Gnomad4 ASJ

AF:

0.0680

Gnomad4 EAS

AF:

0.149

Gnomad4 SAS

AF:

0.0265

Gnomad4 FIN

AF:

0.0191

Gnomad4 NFE

AF:

0.0197

Gnomad4 OTH

AF:

0.0804

Alfa

AF:

0.0394

Hom.:

388

Bravo

AF:

0.0919

Asia WGS

AF:

0.0850

AC:

295

AN:

3478

EpiCase

AF:

0.0249

EpiControl

AF:

0.0254

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

0.91

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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