rs11750092

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000679.4(ADRA1B):​c.949+23110C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,152 control chromosomes in the GnomAD database, including 1,496 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 0.13 ( 1496 hom., cov: 32)

Consequence

ADRA1B
NM_000679.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.10
Variant links:
Genes affected
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ADRA1BNM_000679.4 linkuse as main transcriptc.949+23110C>T intron_variant ENST00000306675.5 NP_000670.1 P35368

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ADRA1BENST00000306675.5 linkuse as main transcriptc.949+23110C>T intron_variant 1 NM_000679.4 ENSP00000306662.3 P35368

Frequencies

GnomAD3 genomes
AF:
0.131
AC:
19857
AN:
152034
Hom.:
1499
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0742
Gnomad AMI
AF:
0.168
Gnomad AMR
AF:
0.103
Gnomad ASJ
AF:
0.141
Gnomad EAS
AF:
0.0457
Gnomad SAS
AF:
0.0899
Gnomad FIN
AF:
0.231
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.164
Gnomad OTH
AF:
0.134
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.131
AC:
19859
AN:
152152
Hom.:
1496
Cov.:
32
AF XY:
0.132
AC XY:
9855
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.0741
Gnomad4 AMR
AF:
0.103
Gnomad4 ASJ
AF:
0.141
Gnomad4 EAS
AF:
0.0456
Gnomad4 SAS
AF:
0.0906
Gnomad4 FIN
AF:
0.231
Gnomad4 NFE
AF:
0.164
Gnomad4 OTH
AF:
0.132
Alfa
AF:
0.145
Hom.:
225
Bravo
AF:
0.116
Asia WGS
AF:
0.0840
AC:
294
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.54
DANN
Benign
0.47

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11750092; hg19: chr5-159367971; API