11-5245498-C-T

Variant names:

• chr11-5245498-C-T
• rs7924684
• ENST00000564523.2:n.49G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ENSG00000290652 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_121648.1. 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
	BGLT3	NR_121648.1		n.49G>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BGLT3	ENST00000564523.2	TSL:6	n.49G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000290652	ENST00000759251.1		n.472+1738G>A		intron	N/A
	ENSG00000290652	ENST00000759252.1		n.244+1738G>A		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.224 AC: 9289 AN: 41470

American (AMR) AF: 0.572 AC: 8735 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2165 AN: 3470

East Asian (EAS) AF: 0.775 AC: 3990 AN: 5148

South Asian (SAS) AF: 0.543 AC: 2600 AN: 4790

European-Finnish (FIN) AF: 0.459 AC: 4854 AN: 10568

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31916 AN: 67916

Other (OTH) AF: 0.490 AC: 1032 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.3
DANN	Benign	0.71
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs7924684; hg19: chr11-5266728;