Genetic Variant ENST00000759251.1:n.473-1122C>T (chr11-5244450-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000759251.1(ENSG00000290652):n.473-1122C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,746 control chromosomes in the GnomAD database, including 7,027 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 0.30 ( 7023 hom., cov: 31)

Exomes 𝑓: 0.29 ( 4 hom. )

Consequence

ENSG00000290652
ENST00000759251.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.806

Publications

3 publications found

Variant links:

COSMIC-nc: COSV57964243

Genes affected

ENSG00000290652 (HGNC:):

ENSG00000290652 links:

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

BGLT3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BGLT3	NR_121648.1 link	n.*104C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000290652	ENST00000759251.1 link	n.473-1122C>T	intron_variant	Intron 1 of 2
ENSG00000290652	ENST00000759252.1 link	n.245-1122C>T	intron_variant	Intron 2 of 3
ENSG00000290652	ENST00000759253.1 link	n.260-1122C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.299

AC:

45282

AN:

151586

Hom.:

7008

Cov.:

show subpopulations

Gnomad AFR

AF:

0.313

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.281

Gnomad ASJ

AF:

0.201

Gnomad EAS

AF:

0.200

Gnomad SAS

AF:

0.287

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.223

Gnomad NFE

AF:

0.321

Gnomad OTH

AF:

0.291

GnomAD4 exome

AF:

0.286

AC:

AN:

Hom.:

AF XY:

0.263

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.237

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.299

AC:

45334

AN:

151704

Hom.:

7023

Cov.:

AF XY:

0.293

AC XY:

21754

AN XY:

74126

show subpopulations

African (AFR)

AF:

0.313

AC:

12934

AN:

41358

American (AMR)

AF:

0.281

AC:

4285

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.201

AC:

696

AN:

3462

East Asian (EAS)

AF:

0.200

AC:

1029

AN:

5150

South Asian (SAS)

AF:

0.287

AC:

1382

AN:

4814

European-Finnish (FIN)

AF:

0.219

AC:

2289

AN:

10462

Middle Eastern (MID)

AF:

0.233

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.321

AC:

21813

AN:

67906

Other (OTH)

AF:

0.297

AC:

623

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1572

3144

4715

6287

7859

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

458

916

1374

1832

2290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.313

Hom.:

942

Bravo

AF:

0.304

Asia WGS

AF:

0.316

AC:

1096

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.1

(source)

DANN

Benign

0.81

PhyloP100

-0.81

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over