rs4135150

chr12-103989821-T-C

Variant summary

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

The NM_001384711.1(GLT8D2):c.881-244A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0841 in 152,026 control chromosomes in the GnomAD database, including 831 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 0.084 (831 hom., cov: 31)
• Consequence: GLT8D2 NM_001384711.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLT8D2	NM_001384711.1	c.881-244A>G		intron_variant		ENST00000360814.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLT8D2	ENST00000360814.9	c.881-244A>G		intron_variant		1	NM_001384711.1	P1
GLT8D2	ENST00000546436.5	c.881-244A>G		intron_variant		5		P1
GLT8D2	ENST00000548660.5	c.881-244A>G		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.0841 AC: 12775 AN: 151908 Hom.: 831 Cov.: 31

Gnomad AFR AF: 0.0199

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.0997

Gnomad ASJ AF: 0.0648

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0999

Gnomad OTH AF: 0.0799

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

GnomAD4 genome AF: 0.0841 AC: 12779 AN: 152026 Hom.: 831 Cov.: 31 AF XY: 0.0868 AC XY: 6456 AN XY: 74336

Gnomad4 AFR AF: 0.0198

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.0648

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.0939

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.0795

Alfa AF: 0.0931 Hom.: 150

Bravo AF: 0.0828

Asia WGS AF: 0.168 AC: 582 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.5
Dann	Benign	0.81

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

Other links and lift over

dbSNP: rs4135150; hg19: chr12-104383599;