rs4937877

chr11-134365498-G-Achr11-134365498-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001370461.1(GLB1L2):c.804+1100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 152,134 control chromosomes in the GnomAD database, including 36,962 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 0.69 (36962 hom., cov: 33)
• Consequence: GLB1L2 NM_001370461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

GLB1L2 (HGNC:25129): (galactosidase beta 1 like 2) Predicted to enable beta-galactosidase activity. Predicted to be involved in carbohydrate metabolic process. Predicted to be located in extracellular region. 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 (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLB1L2	NM_001370461.1	c.804+1100G>A		intron_variant		ENST00000535456.7
GLB1L2	NM_001370460.1	c.966+1100G>A		intron_variant
GLB1L2	NM_138342.4	c.804+1100G>A		intron_variant
GLB1L2	XR_007062523.1	n.878+1100G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLB1L2	ENST00000535456.7	c.804+1100G>A		intron_variant		1	NM_001370461.1	P1
GLB1L2	ENST00000529077.5	n.2879+1100G>A		intron_variant, non_coding_transcript_variant		1
GLB1L2	ENST00000533324.2	n.286+1100G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105451 AN: 152016 Hom.: 36917 Cov.: 33

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.694 AC: 105556 AN: 152134 Hom.: 36962 Cov.: 33 AF XY: 0.697 AC XY: 51856 AN XY: 74368

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.710

Alfa AF: 0.680 Hom.: 46388

Bravo AF: 0.701

Asia WGS AF: 0.861 AC: 2993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.15
Dann	Benign	0.47

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: rs4937877; hg19: chr11-134235392;