11-134374229-C-T

Variant names:

• chr11-134374229-C-T
• rs3741097
• NM_001370461.1:c.1680C>T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_001370461.1(GLB1L2):​c.1680C>T​(p.Thr560Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: GLB1L2 NM_001370461.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318
• Publications: 18 publications found

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

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.049).
• BP7: Synonymous conserved (PhyloP=0.318 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLB1L2	NM_001370461.1	c.1680C>T	p.Thr560Thr	synonymous_variant	Exon 17 of 19	ENST00000535456.7	NP_001357390.1
GLB1L2	NM_001370460.1	c.1842C>T	p.Thr614Thr	synonymous_variant	Exon 18 of 20		NP_001357389.1
GLB1L2	NM_138342.4	c.1680C>T	p.Thr560Thr	synonymous_variant	Exon 17 of 20		NP_612351.2
GLB1L2	XR_007062523.1	n.1754C>T		non_coding_transcript_exon_variant	Exon 17 of 20

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLB1L2	ENST00000535456.7	c.1680C>T	p.Thr560Thr	synonymous_variant	Exon 17 of 19	1	NM_001370461.1	ENSP00000444628.1
GLB1L2	ENST00000529077.5	n.4009C>T		non_coding_transcript_exon_variant	Exon 18 of 22	1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.1
DANN	Benign	0.64
PhyloP100		0.32

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: rs3741097; hg19: chr11-134244123;