chr12-128936520-A-G

Variant names:

• chr12-128936520-A-G
• rs11060028
• NM_001366886.1:c.616-8806A>G

Variant summary

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

The NM_001366886.1(GLT1D1):​c.616-8806A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,194 control chromosomes in the GnomAD database, including 1,673 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 0.13 (1673 hom., cov: 32)
• Consequence: GLT1D1 NM_001366886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 3 publications found

Genes affected

GLT1D1 (HGNC:26483): (glycosyltransferase 1 domain containing 1) Predicted to enable glycosyltransferase activity. Located in cytosol. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366886.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLT1D1	NM_001366886.1	MANE Select	c.616-8806A>G		intron	N/A	NP_001353815.1
	GLT1D1	NM_001366889.1		c.664-8806A>G		intron	N/A	NP_001353818.1
	GLT1D1	NM_001366887.1		c.490-8806A>G		intron	N/A	NP_001353816.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLT1D1	ENST00000442111.7	TSL:5 MANE Select	c.616-8806A>G		intron	N/A	ENSP00000394692.2
	GLT1D1	ENST00000441390.6	TSL:1	n.*105-8806A>G		intron	N/A	ENSP00000411992.2
	GLT1D1	ENST00000905390.1		c.664-8806A>G		intron	N/A	ENSP00000575449.1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20460 AN: 152076 Hom.: 1670 Cov.: 32

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.134 AC: 20460 AN: 152194 Hom.: 1673 Cov.: 32 AF XY: 0.140 AC XY: 10445 AN XY: 74408

African (AFR) AF: 0.0910 AC: 3780 AN: 41534

American (AMR) AF: 0.209 AC: 3201 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3466

East Asian (EAS) AF: 0.343 AC: 1771 AN: 5158

South Asian (SAS) AF: 0.259 AC: 1247 AN: 4820

European-Finnish (FIN) AF: 0.109 AC: 1153 AN: 10604

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8452 AN: 68016

Other (OTH) AF: 0.120 AC: 253 AN: 2106

Alfa AF: 0.119 Hom.: 444

Bravo AF: 0.141

Asia WGS AF: 0.284 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.45
PhyloP100		0.11
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: rs11060028; hg19: chr12-129421065;