chr12-104028030-A-G

Variant names:

• chr12-104028030-A-G
• rs2629751
• NM_001384711.1:c.-163-6539T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001384711.1(GLT8D2):​c.-163-6539T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,048 control chromosomes in the GnomAD database, including 10,146 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 (10146 hom., cov: 32)
• Consequence: GLT8D2 NM_001384711.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 11 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001384711.1. 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_001384711.1	MANE Select	c.-163-6539T>C		intron	N/A	NP_001371640.1
	GLT8D2	NM_001384712.1		c.-28-8354T>C		intron	N/A	NP_001371641.1
	GLT8D2	NM_001316967.2		c.-28-8354T>C		intron	N/A	NP_001303896.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLT8D2	ENST00000360814.9	TSL:1 MANE Select	c.-163-6539T>C		intron	N/A	ENSP00000354053.4
	GLT8D2	ENST00000546436.5	TSL:5	c.-29+1666T>C		intron	N/A	ENSP00000449750.1
	GLT8D2	ENST00000548660.5	TSL:2	c.-28-8354T>C		intron	N/A	ENSP00000447450.1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54356 AN: 151930 Hom.: 10131 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.358 AC: 54410 AN: 152048 Hom.: 10146 Cov.: 32 AF XY: 0.352 AC XY: 26198 AN XY: 74342

African (AFR) AF: 0.439 AC: 18209 AN: 41446

American (AMR) AF: 0.386 AC: 5895 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1315 AN: 3468

East Asian (EAS) AF: 0.309 AC: 1597 AN: 5176

South Asian (SAS) AF: 0.322 AC: 1554 AN: 4826

European-Finnish (FIN) AF: 0.253 AC: 2682 AN: 10584

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.322 AC: 21858 AN: 67968

Other (OTH) AF: 0.344 AC: 727 AN: 2114

Alfa AF: 0.353 Hom.: 9749

Bravo AF: 0.375

Asia WGS AF: 0.317 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.4
DANN	Benign	0.68
PhyloP100		0.23
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2629751; hg19: chr12-104421808;