dbSNP rs11036415: ENSG00000290652:n.1003T>G (chr11-5241552-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000454892.2(ENSG00000290652):n.1003T>G 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 0.817 in 152,058 control chromosomes in the GnomAD database, including 50,881 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 0.82 ( 50864 hom., cov: 30)

Exomes 𝑓: 0.81 ( 17 hom. )

Consequence

ENSG00000290652
ENST00000454892.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07

Publications

3 publications found

Variant links:

Genes affected

ENSG00000290652 (HGNC:):

ENSG00000290652 links:

HBD (HGNC:4829): (hemoglobin subunit delta) The delta (HBD) and beta (HBB) genes are normally expressed in the adult: two alpha chains plus two beta chains constitute HbA, which in normal adult life comprises about 97% of the total hemoglobin. Two alpha chains plus two delta chains constitute HbA-2, which with HbF comprises the remaining 3% of adult hemoglobin. Five beta-like globin genes are found within a 45 kb cluster on chromosome 11 in the following order: 5'-epsilon--Ggamma--Agamma--delta--beta-3'. Mutations in the delta-globin gene are associated with beta-thalassemia. [provided by RefSeq, Jul 2008]

HBD Gene-Disease associations (from GenCC):

delta-beta-thalassemia
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

HBD links:

Genome browser will be placed here

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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein
ENSG00000290652	ENST00000454892.2 link	n.1003T>G	non_coding_transcript_exon_variant	Exon 3 of 3	2
HBD	ENST00000643122.1 link	c.-29+1898T>G	intron_variant	Intron 1 of 3		ENSP00000494708.1
ENSG00000298932	ENST00000759072.1 link	n.266-1557A>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.817

AC:

124108

AN:

151886

Hom.:

50820

Cov.:

show subpopulations

Gnomad AFR

AF:

0.818

Gnomad AMI

AF:

0.780

Gnomad AMR

AF:

0.863

Gnomad ASJ

AF:

0.869

Gnomad EAS

AF:

0.898

Gnomad SAS

AF:

0.832

Gnomad FIN

AF:

0.683

Gnomad MID

AF:

0.877

Gnomad NFE

AF:

0.816

Gnomad OTH

AF:

0.857

GnomAD4 exome

AF:

0.815

AC:

AN:

Hom.:

Cov.:

AF XY:

0.813

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.833

AC:

AN:

Other (OTH)

AF:

0.833

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.590

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.817

AC:

124214

AN:

152004

Hom.:

50864

Cov.:

AF XY:

0.813

AC XY:

60417

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.818

AC:

33881

AN:

41436

American (AMR)

AF:

0.863

AC:

13197

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.869

AC:

3017

AN:

3470

East Asian (EAS)

AF:

0.898

AC:

4638

AN:

5164

South Asian (SAS)

AF:

0.833

AC:

4011

AN:

4818

European-Finnish (FIN)

AF:

0.683

AC:

7210

AN:

10552

Middle Eastern (MID)

AF:

0.871

AC:

256

AN:

294

European-Non Finnish (NFE)

AF:

0.816

AC:

55478

AN:

67962

Other (OTH)

AF:

0.860

AC:

1816

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1180

2359

3539

4718

5898

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

878

1756

2634

3512

4390

<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:

0.816

Hom.:

10270

Bravo

AF:

0.825

Asia WGS

AF:

0.865

AC:

3008

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.48

(source)

DANN

Benign

0.40

PhyloP100

-1.1

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over