dbSNP rs10077860: LINC01847:n.80A>T (chr5-159871305-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000865014.1(ADRA1B):c.-390+6099T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,168 control chromosomes in the GnomAD database, including 1,164 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 0.11 ( 1164 hom., cov: 32)

Exomes 𝑓: 0.083 ( 0 hom. )

Consequence

ADRA1B
ENST00000865014.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00600

Publications

1 publications found

Variant links:

Genes affected

LINC01847 (HGNC:52662): (long intergenic non-protein coding RNA 1847)

LINC01847 links:

ADRA1B (HGNC:278): (adrenoceptor alpha 1B) Alpha-1-adrenergic receptors (alpha-1-ARs) are members of the G protein-coupled receptor superfamily. They activate mitogenic responses and regulate growth and proliferation of many cells. There are 3 alpha-1-AR subtypes: alpha-1A, -1B and -1D, all of which signal through the Gq/11 family of G-proteins and different subtypes show different patterns of activation. This gene encodes alpha-1B-adrenergic receptor, which induces neoplastic transformation when transfected into NIH 3T3 fibroblasts and other cell lines. Thus, this normal cellular gene is identified as a protooncogene. This gene comprises 2 exons and a single large intron of at least 20 kb that interrupts the coding region. [provided by RefSeq, Jul 2008]

ADRA1B 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000865014.1. 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
	LINC01847	NR_109891.1		n.80A>T		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LINC01847	ENST00000522627.1	TSL:1	n.80A>T	non_coding_transcript_exon	Exon 1 of 3
ADRA1B	ENST00000865014.1		c.-390+6099T>A	intron	N/A	ENSP00000535073.1
ADRA1B	ENST00000641205.1		c.-256+6099T>A	intron	N/A	ENSP00000493019.1	A0A286YF88

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16254

AN:

152038

Hom.:

1162

Cov.:

show subpopulations

Gnomad AFR

AF:

0.203

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.0778

Gnomad ASJ

AF:

0.0813

Gnomad EAS

AF:

0.0233

Gnomad SAS

AF:

0.0720

Gnomad FIN

AF:

0.0672

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0716

Gnomad OTH

AF:

0.0953

GnomAD4 exome

AF:

0.0833

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0833

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)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0833

AC:

AN:

Other (OTH)

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:

0.107

AC:

16285

AN:

152156

Hom.:

1164

Cov.:

AF XY:

0.106

AC XY:

7917

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.203

AC:

8435

AN:

41492

American (AMR)

AF:

0.0776

AC:

1187

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0813

AC:

282

AN:

3470

East Asian (EAS)

AF:

0.0233

AC:

121

AN:

5188

South Asian (SAS)

AF:

0.0721

AC:

346

AN:

4802

European-Finnish (FIN)

AF:

0.0672

AC:

712

AN:

10596

Middle Eastern (MID)

AF:

0.0782

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0716

AC:

4869

AN:

68004

Other (OTH)

AF:

0.0938

AC:

198

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

727

1454

2180

2907

3634

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

328

492

656

820

<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:

0.0949

Hom.:

112

Bravo

AF:

0.111

Asia WGS

AF:

0.0520

AC:

181

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.56

(source)

DANN

Benign

0.59

PhyloP100

0.0060

Mutation Taster

=99/1

polymorphism

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over