NM_001370461.1:c.1508-168C>T

Variant names:

• chr11-134373553-C-T
• rs3741098
• NM_001370461.1:c.1508-168C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
GLB1L2	NM_001370461.1	c.1508-168C>T		intron_variant	Intron 15 of 18	ENST00000535456.7	NP_001357390.1
GLB1L2	NM_001370460.1	c.1670-168C>T		intron_variant	Intron 16 of 19		NP_001357389.1
GLB1L2	NM_138342.4	c.1508-168C>T		intron_variant	Intron 15 of 19		NP_612351.2
GLB1L2	XR_007062523.1	n.1582-168C>T		intron_variant	Intron 15 of 19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLB1L2	ENST00000535456.7	c.1508-168C>T		intron_variant	Intron 15 of 18	1	NM_001370461.1	ENSP00000444628.1
GLB1L2	ENST00000529077.5	n.3837-168C>T		intron_variant	Intron 16 of 21	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

African (AFR) AF: 0.197 AC: 8157 AN: 41482

American (AMR) AF: 0.196 AC: 2996 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 818 AN: 3472

East Asian (EAS) AF: 0.504 AC: 2586 AN: 5130

South Asian (SAS) AF: 0.382 AC: 1839 AN: 4814

European-Finnish (FIN) AF: 0.200 AC: 2119 AN: 10594

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14597 AN: 67948

Other (OTH) AF: 0.217 AC: 458 AN: 2110

Alfa AF: 0.209 Hom.: 3775

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
PhyloP100		-0.39
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: rs3741098; hg19: chr11-134243447;