NM_000680.4:c.883+25987G>T

Variant names:

• chr8-26838100-C-A
• rs10503800
• NM_000680.4:c.883+25987G>T

Variant summary

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

The NM_000680.4(ADRA1A):​c.883+25987G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,054 control chromosomes in the GnomAD database, including 9,716 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 0.35 (9716 hom., cov: 33)
• Consequence: ADRA1A NM_000680.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 11 publications found

Genes affected

ADRA1A (HGNC:277): (adrenoceptor alpha 1A) 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-1A-adrenergic receptor. Alternative splicing of this gene generates four transcript variants, which encode four different isoforms with distinct C-termini but having similar ligand binding properties. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADRA1A	NM_000680.4	c.883+25987G>T		intron_variant	Intron 2 of 2	ENST00000380573.4	NP_000671.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADRA1A	ENST00000380573.4	c.883+25987G>T		intron_variant	Intron 2 of 2	2	NM_000680.4	ENSP00000369947.3

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53441 AN: 151936 Hom.: 9703 Cov.: 33

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.352 AC: 53496 AN: 152054 Hom.: 9716 Cov.: 33 AF XY: 0.355 AC XY: 26358 AN XY: 74342

African (AFR) AF: 0.428 AC: 17725 AN: 41430

American (AMR) AF: 0.360 AC: 5500 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1196 AN: 3472

East Asian (EAS) AF: 0.445 AC: 2305 AN: 5174

South Asian (SAS) AF: 0.423 AC: 2036 AN: 4818

European-Finnish (FIN) AF: 0.278 AC: 2943 AN: 10582

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20713 AN: 67982

Other (OTH) AF: 0.366 AC: 773 AN: 2114

Alfa AF: 0.321 Hom.: 30398

Bravo AF: 0.359

Asia WGS AF: 0.458 AC: 1594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	2.2
DANN	Benign	0.74
PhyloP100		-0.13
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: rs10503800; hg19: chr8-26695617;