Genetic Variant GLT8D2:p.Leu196Leu (chr12-103996747-G-A) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_001384711.1(GLT8D2):c.588C>T(p.Leu196Leu) 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

Publications

12 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GLT8D2	NM_001384711.1 link	c.588C>T	p.Leu196Leu	synonymous_variant	Exon 8 of 11	ENST00000360814.9	NP_001371640.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
GLT8D2	ENST00000360814.9 link	c.588C>T	p.Leu196Leu	synonymous_variant	Exon 8 of 11	1	NM_001384711.1	ENSP00000354053.4	Q9H1C3
GLT8D2	ENST00000546436.5 link	c.588C>T	p.Leu196Leu	synonymous_variant	Exon 7 of 10	5		ENSP00000449750.1	Q9H1C3
GLT8D2	ENST00000548660.5 link	c.588C>T	p.Leu196Leu	synonymous_variant	Exon 8 of 11	2		ENSP00000447450.1	Q9H1C3
GLT8D2	ENST00000552572.1 link	n.100C>T		non_coding_transcript_exon_variant	Exon 1 of 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

GnomAD2 exomes

AF:

0.0504

AC:

12645

AN:

250692

AF XY:

0.0457

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 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

African (AFR)

AF:

0.208

AC:

6940

AN:

33396

American (AMR)

AF:

0.0587

AC:

2617

AN:

44562

Ashkenazi Jewish (ASJ)

AF:

0.0617

AC:

1610

AN:

26100

East Asian (EAS)

AF:

0.169

AC:

6684

AN:

39654

South Asian (SAS)

AF:

0.0256

AC:

2204

AN:

86104

European-Finnish (FIN)

AF:

0.0192

AC:

1023

AN:

53398

Middle Eastern (MID)

AF:

0.0798

AC:

453

AN:

5674

European-Non Finnish (NFE)

AF:

0.0180

AC:

20025

AN:

1110814

Other (OTH)

AF:

0.0452

AC:

2725

AN:

60282

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

1876

3752

5627

7503

9379

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0815

AC:

12410

AN:

152250

Hom.:

1015

Cov.:

AF XY:

0.0814

AC XY:

6065

AN XY:

74468

show subpopulations

African (AFR)

AF:

0.202

AC:

8403

AN:

41516

American (AMR)

AF:

0.0734

AC:

1123

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0680

AC:

236

AN:

3472

East Asian (EAS)

AF:

0.149

AC:

769

AN:

5178

South Asian (SAS)

AF:

0.0265

AC:

128

AN:

4830

European-Finnish (FIN)

AF:

0.0191

AC:

203

AN:

10616

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0197

AC:

1341

AN:

68020

Other (OTH)

AF:

0.0804

AC:

170

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

533

1067

1600

2134

2667

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0440

Hom.:

578

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

(source)

DANN

Benign

0.71

PhyloP100

-0.80

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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12-103996747-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over