11-134373553-C-T

Position:

• chr11-134373553-C-T

Variant summary

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

The NM_001370461.1(GLB1L2):​c.1508-168C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,042 control chromosomes in the GnomAD database, including 4,096 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 0.22 (4096 hom., cov: 33)
• Consequence: GLB1L2 NM_001370461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.390

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLB1L2	NM_001370461.1	c.1508-168C>T		intron_variant		ENST00000535456.7
GLB1L2	NM_001370460.1	c.1670-168C>T		intron_variant
GLB1L2	NM_138342.4	c.1508-168C>T		intron_variant
GLB1L2	XR_007062523.1	n.1582-168C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLB1L2	ENST00000535456.7	c.1508-168C>T		intron_variant		1	NM_001370461.1	P1
GLB1L2	ENST00000529077.5	n.3837-168C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33786 AN: 151924 Hom.: 4092 Cov.: 33

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.222 AC: 33807 AN: 152042 Hom.: 4096 Cov.: 33 AF XY: 0.227 AC XY: 16843 AN XY: 74304

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.217

Alfa AF: 0.210 Hom.: 2913

Bravo AF: 0.216

Asia WGS AF: 0.390 AC: 1351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.74

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: rs3741098; hg19: chr11-134243447;