rs1893054

Positions:

• chr11-134303852-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLB1L3	NM_001080407.3	c.877-3272T>C		intron_variant		ENST00000431683.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLB1L3	ENST00000431683.7	c.877-3272T>C		intron_variant		5	NM_001080407.3	P1
GLB1L3	ENST00000389887.9	c.877-1263T>C		intron_variant		1
GLB1L3	ENST00000486034.5	n.452-3272T>C		intron_variant, non_coding_transcript_variant		2
GLB1L3	ENST00000498012.5	n.1360-8497T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.292

Alfa AF: 0.229 Hom.: 8766

Bravo AF: 0.320

Asia WGS AF: 0.365 AC: 1268 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.1
DANN	Benign	0.55

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

Publications

LitVar

Other links and lift over

dbSNP: rs1893054; hg19: chr11-134173746; COSMIC: COSV66280820; COSMIC: COSV66280820;