chr12-104051964-A-G

Variant names:

• chr12-104051964-A-G
• rs1564892
• XM_047429629.1:c.-2233T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031302.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLT8D2	NM_001316967.2		c.-422-1676T>C		intron	N/A	NP_001303896.1
	GLT8D2	NM_001384713.1		c.-824-1409T>C		intron	N/A	NP_001371642.1
	GLT8D2	NM_001384715.1		c.-824-1409T>C		intron	N/A	NP_001371644.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLT8D2	ENST00000548660.5	TSL:2	c.-422-1676T>C		intron	N/A	ENSP00000447450.1
	GLT8D2	ENST00000879067.1		c.-689-1409T>C		intron	N/A	ENSP00000549126.1
	GLT8D2	ENST00000879068.1		c.-164+11985T>C		intron	N/A	ENSP00000549127.1

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

African (AFR) AF: 0.562 AC: 23274 AN: 41446

American (AMR) AF: 0.292 AC: 4459 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1109 AN: 3472

East Asian (EAS) AF: 0.681 AC: 3530 AN: 5184

South Asian (SAS) AF: 0.463 AC: 2233 AN: 4824

European-Finnish (FIN) AF: 0.238 AC: 2512 AN: 10538

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16187 AN: 67984

Other (OTH) AF: 0.335 AC: 708 AN: 2112

Alfa AF: 0.301 Hom.: 3662

Bravo AF: 0.367

Asia WGS AF: 0.578 AC: 1997 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.7
DANN	Benign	0.83
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1564892; hg19: chr12-104445742;