NM_001080407.3:c.877-3272T>C

Variant names:

• chr11-134303852-T-C
• rs1893054
• NM_001080407.3:c.877-3272T>C

Variant summary

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

The NM_001080407.3(GLB1L3):​c.877-3272T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 151,836 control chromosomes in the GnomAD database, including 8,097 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 0.31 (8097 hom., cov: 32)
• Consequence: GLB1L3 NM_001080407.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.633
• Publications: 6 publications found

Genes affected

GLB1L3 (HGNC:25147): (galactosidase beta 1 like 3) Predicted to enable beta-galactosidase activity. Predicted to be involved in carbohydrate metabolic process. Predicted to be active in vacuole. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080407.3. 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
	GLB1L3	NM_001080407.3	MANE Select	c.877-3272T>C		intron	N/A	NP_001073876.2	Q8NCI6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLB1L3	ENST00000431683.7	TSL:5 MANE Select	c.877-3272T>C		intron	N/A	ENSP00000396615.2	Q8NCI6-1
	GLB1L3	ENST00000389887.9	TSL:1	c.877-1263T>C		intron	N/A	ENSP00000374537.5	Q8NCI6-4
	GLB1L3	ENST00000927565.1		c.877-3272T>C		intron	N/A	ENSP00000597624.1

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46302 AN: 151718 Hom.: 8082 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.305 AC: 46359 AN: 151836 Hom.: 8097 Cov.: 32 AF XY: 0.306 AC XY: 22728 AN XY: 74194

African (AFR) AF: 0.482 AC: 19912 AN: 41316

American (AMR) AF: 0.315 AC: 4813 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 657 AN: 3470

East Asian (EAS) AF: 0.340 AC: 1752 AN: 5148

South Asian (SAS) AF: 0.344 AC: 1656 AN: 4814

European-Finnish (FIN) AF: 0.221 AC: 2324 AN: 10534

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14367 AN: 67966

Other (OTH) AF: 0.292 AC: 617 AN: 2114

Alfa AF: 0.247 Hom.: 16289

Bravo AF: 0.320

Asia WGS AF: 0.365 AC: 1268 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.1
DANN	Benign	0.55
PhyloP100		0.63
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: rs1893054; hg19: chr11-134173746; COSMIC: COSV66280820; COSMIC: COSV66280820;