5-159895916-G-A

Variant names:

• chr5-159895916-G-A
• rs2195926
• ENST00000641205.1:c.-255-20203G>A

Variant summary

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

The ENST00000641205.1(ADRA1B):​c.-255-20203G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 152,102 control chromosomes in the GnomAD database, including 39,660 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 0.70 (39660 hom., cov: 32)
• Consequence: ADRA1B ENST00000641205.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641205.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADRA1B	ENST00000641205.1		c.-255-20203G>A		intron	N/A	ENSP00000493019.1
	LINC01847	ENST00000641163.1		n.182-27988C>T		intron	N/A
	LINC01847	ENST00000816795.1		n.143-27988C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.704 AC: 107042 AN: 151986 Hom.: 39618 Cov.: 32

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.704 AC: 107122 AN: 152102 Hom.: 39660 Cov.: 32 AF XY: 0.694 AC XY: 51581 AN XY: 74358

African (AFR) AF: 0.885 AC: 36752 AN: 41512

American (AMR) AF: 0.551 AC: 8431 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2472 AN: 3466

East Asian (EAS) AF: 0.204 AC: 1053 AN: 5170

South Asian (SAS) AF: 0.527 AC: 2538 AN: 4814

European-Finnish (FIN) AF: 0.627 AC: 6624 AN: 10566

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46917 AN: 67968

Other (OTH) AF: 0.697 AC: 1471 AN: 2110

Alfa AF: 0.649 Hom.: 2412

Bravo AF: 0.703

Asia WGS AF: 0.417 AC: 1452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.34
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs2195926; hg19: chr5-159322923;