rs11059985

Variant names:

• chr12-128863346-G-A
• rs11059985
• NM_001366886.1:c.68+9697G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-128863346-G-A
• chr12-128863346-G-T

Variant summary

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

The NM_001366886.1(GLT1D1):​c.68+9697G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,752 control chromosomes in the GnomAD database, including 6,540 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 0.29 (6540 hom., cov: 31)
• Consequence: GLT1D1 NM_001366886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 4 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.512 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.68+9697G>A		intron	N/A	NP_001353815.1	Q96MS3-1
	GLT1D1	NM_001366889.1		c.68+9697G>A		intron	N/A	NP_001353818.1
	GLT1D1	NM_001366887.1		c.91+9697G>A		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.68+9697G>A		intron	N/A	ENSP00000394692.2	Q96MS3-1
	GLT1D1	ENST00000441390.6	TSL:1	n.68+9697G>A		intron	N/A	ENSP00000411992.2	Q96MS3-3
	GLT1D1	ENST00000905390.1		c.68+9697G>A		intron	N/A	ENSP00000575449.1

Frequencies

GnomAD3 genomes AF: 0.290 AC: 43901 AN: 151640 Hom.: 6517 Cov.: 31

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.290 AC: 43964 AN: 151752 Hom.: 6540 Cov.: 31 AF XY: 0.298 AC XY: 22117 AN XY: 74150

African (AFR) AF: 0.298 AC: 12333 AN: 41364

American (AMR) AF: 0.333 AC: 5079 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1229 AN: 3468

East Asian (EAS) AF: 0.304 AC: 1562 AN: 5136

South Asian (SAS) AF: 0.529 AC: 2534 AN: 4792

European-Finnish (FIN) AF: 0.305 AC: 3213 AN: 10524

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17161 AN: 67926

Other (OTH) AF: 0.301 AC: 634 AN: 2106

Alfa AF: 0.267 Hom.: 24691

Bravo AF: 0.288

Asia WGS AF: 0.427 AC: 1484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.38
PhyloP100		-1.3
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: rs11059985; hg19: chr12-129347891; COSMIC: COSV55888771; COSMIC: COSV55888771;