rs6795737

chr3-32963738-T-G

Variant summary

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

The NM_001393580.1(GLB1):c.1735-2117A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 152,060 control chromosomes in the GnomAD database, including 28,041 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 0.60 (28041 hom., cov: 33)
• Consequence: GLB1 NM_001393580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435

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 (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLB1	NM_001393580.1	c.1735-2117A>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90738 AN: 151942 Hom.: 27981 Cov.: 33

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.598 AC: 90858 AN: 152060 Hom.: 28041 Cov.: 33 AF XY: 0.594 AC XY: 44152 AN XY: 74318

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.581

Alfa AF: 0.541 Hom.: 45273

Bravo AF: 0.596

Asia WGS AF: 0.498 AC: 1736 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	3.4
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6795737; hg19: chr3-33005230;