5-159920474-C-A

Variant names:

• chr5-159920474-C-A
• rs2030373
• NM_000679.4:c.949+2620C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000679.4(ADRA1B):​c.949+2620C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,958 control chromosomes in the GnomAD database, including 5,649 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 0.26 (5649 hom., cov: 32)
• Consequence: ADRA1B NM_000679.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 5 publications found

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]

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADRA1B	NM_000679.4	c.949+2620C>A		intron_variant	Intron 1 of 1	ENST00000306675.5	NP_000670.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADRA1B	ENST00000306675.5	c.949+2620C>A		intron_variant	Intron 1 of 1	1	NM_000679.4	ENSP00000306662.3
LINC01847	ENST00000641163.1	n.181+8561G>T		intron_variant	Intron 2 of 7
LINC01847	ENST00000816795.1	n.142+8561G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39964 AN: 151840 Hom.: 5645 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.263

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.263 AC: 39985 AN: 151958 Hom.: 5649 Cov.: 32 AF XY: 0.265 AC XY: 19698 AN XY: 74254

African (AFR) AF: 0.244 AC: 10115 AN: 41444

American (AMR) AF: 0.308 AC: 4704 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3466

East Asian (EAS) AF: 0.606 AC: 3109 AN: 5132

South Asian (SAS) AF: 0.259 AC: 1245 AN: 4804

European-Finnish (FIN) AF: 0.214 AC: 2257 AN: 10554

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16738 AN: 67986

Other (OTH) AF: 0.265 AC: 560 AN: 2110

Alfa AF: 0.257 Hom.: 22207

Bravo AF: 0.271

Asia WGS AF: 0.412 AC: 1434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.4
DANN	Benign	0.77
PhyloP100		-0.28
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2030373; hg19: chr5-159347481;