rs4937877

Variant names:

• chr11-134365498-G-A
• rs4937877
• NM_001370461.1:c.804+1100G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-134365498-G-A
• chr11-134365498-G-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.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
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370461.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLB1L2	NM_001370461.1	MANE Select	c.804+1100G>A		intron	N/A	NP_001357390.1	Q8IW92
	GLB1L2	NM_001370460.1		c.966+1100G>A		intron	N/A	NP_001357389.1
	GLB1L2	NM_138342.4		c.804+1100G>A		intron	N/A	NP_612351.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLB1L2	ENST00000535456.7	TSL:1 MANE Select	c.804+1100G>A		intron	N/A	ENSP00000444628.1	Q8IW92
	GLB1L2	ENST00000529077.5	TSL:1	n.2879+1100G>A		intron	N/A
	GLB1L2	ENST00000855671.1		c.804+1100G>A		intron	N/A	ENSP00000525730.1

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

African (AFR) AF: 0.695 AC: 28822 AN: 41476

American (AMR) AF: 0.762 AC: 11661 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2458 AN: 3468

East Asian (EAS) AF: 0.925 AC: 4789 AN: 5180

South Asian (SAS) AF: 0.827 AC: 3999 AN: 4834

European-Finnish (FIN) AF: 0.630 AC: 6666 AN: 10574

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 45013 AN: 67984

Other (OTH) AF: 0.710 AC: 1499 AN: 2112

Alfa AF: 0.682 Hom.: 59045

Bravo AF: 0.701

Asia WGS AF: 0.861 AC: 2993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.47
PhyloP100		-1.2
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: rs4937877; hg19: chr11-134235392;