11-5245498-C-T

Variant summary

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

The NR_121648.1(BGLT3):n.49G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,944 control chromosomes in the GnomAD database, including 15,639 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 0.43 (15639 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: BGLT3 NR_121648.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

BGLT3 (HGNC:49033): (beta globin locus transcript 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BGLT3	NR_121648.1	n.49G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BGLT3	ENST00000564523.2	n.49G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65200 AN: 151824 Hom.: 15628 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.488

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.429 AC: 65248 AN: 151944 Hom.: 15639 Cov.: 31 AF XY: 0.436 AC XY: 32388 AN XY: 74264

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.490

Alfa AF: 0.436 Hom.: 1899

Bravo AF: 0.428

Asia WGS AF: 0.598 AC: 2078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	2.3
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7924684; hg19: chr11-5266728;