rs1564892

Positions:

• chr12-104051964-A-G

Variant summary

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

The NM_031302.5(GLT8D2):​c.-557-1676T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,042 control chromosomes in the GnomAD database, including 11,552 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 0.36 (11552 hom., cov: 33)
• Consequence: GLT8D2 NM_031302.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLT8D2	XM_047429629.1	c.-2233T>C		5_prime_UTR_variant	2/12		XP_047285585.1
GLT8D2	XM_047429630.1	c.-2303T>C		5_prime_UTR_variant	2/13		XP_047285586.1
GLT8D2	XM_047429631.1	c.-2098T>C		5_prime_UTR_variant	2/11		XP_047285587.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLT8D2	ENST00000548660.5	c.-422-1676T>C		intron_variant		2		ENSP00000447450.1

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54163 AN: 151924 Hom.: 11528 Cov.: 33

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.357 AC: 54233 AN: 152042 Hom.: 11552 Cov.: 33 AF XY: 0.359 AC XY: 26699 AN XY: 74322

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.335

Alfa AF: 0.278 Hom.: 1812

Bravo AF: 0.367

Asia WGS AF: 0.578 AC: 1997 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.7
DANN	Benign	0.83

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1564892; hg19: chr12-104445742;