12-128922040-C-T

Variant names:

• chr12-128922040-C-T
• rs1465727
• NM_144669.3:c.375+22753C>T

Variant summary

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

The NM_144669.3(GLT1D1):​c.375+22753C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,504 control chromosomes in the GnomAD database, including 26,122 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 0.57 (26122 hom., cov: 29)
• Consequence: GLT1D1 NM_144669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.945
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLT1D1	NM_144669.3	c.375+22753C>T		intron_variant	Intron 4 of 7	ENST00000281703.11	NP_653270.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLT1D1	ENST00000281703.11	c.375+22753C>T		intron_variant	Intron 4 of 7	2	NM_144669.3	ENSP00000281703.6
GLT1D1	ENST00000442111.7	c.470-4319C>T		intron_variant	Intron 6 of 11	5		ENSP00000394692.2

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86346 AN: 151386 Hom.: 26105 Cov.: 29

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.570 AC: 86402 AN: 151504 Hom.: 26122 Cov.: 29 AF XY: 0.566 AC XY: 41854 AN XY: 73986

African (AFR) AF: 0.390 AC: 16099 AN: 41230

American (AMR) AF: 0.553 AC: 8412 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1854 AN: 3466

East Asian (EAS) AF: 0.328 AC: 1688 AN: 5146

South Asian (SAS) AF: 0.438 AC: 2095 AN: 4788

European-Finnish (FIN) AF: 0.695 AC: 7259 AN: 10452

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47132 AN: 67896

Other (OTH) AF: 0.549 AC: 1155 AN: 2104

Alfa AF: 0.650 Hom.: 31545

Bravo AF: 0.551

Asia WGS AF: 0.393 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.51
DANN	Benign	0.56
PhyloP100		-0.94
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: rs1465727; hg19: chr12-129406585;