3-32978543-G-T

Variant summary

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

The NM_001393580.1(GLB1):c.1735-16922C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,030 control chromosomes in the GnomAD database, including 43,554 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 0.74 (43554 hom., cov: 31)
• Consequence: GLB1 NM_001393580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

Genes affected

GLB1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLB1	NM_001393580.1	c.1735-16922C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112152 AN: 151912 Hom.: 43514 Cov.: 31

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.738 AC: 112246 AN: 152030 Hom.: 43554 Cov.: 31 AF XY: 0.746 AC XY: 55445 AN XY: 74316

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.899

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.750

Alfa AF: 0.816 Hom.: 98123

Bravo AF: 0.718

Asia WGS AF: 0.828 AC: 2878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.8
Dann	Benign	0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4678680; hg19: chr3-33020035;