rs657561

Variant names:

• chr11-75309335-T-C
• rs657561
• NM_004041.5:c.21-19296A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-75309335-T-C
• chr11-75309335-T-G

Variant summary

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

The NM_004041.5(ARRB1):​c.21-19296A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,246 control chromosomes in the GnomAD database, including 32,141 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 0.64 (32141 hom., cov: 36)
• Consequence: ARRB1 NM_004041.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 3 publications found

Genes affected

ARRB1 (HGNC:711): (arrestin beta 1) Members of arrestin/beta-arrestin protein family are thought to participate in agonist-mediated desensitization of G-protein-coupled receptors and cause specific dampening of cellular responses to stimuli such as hormones, neurotransmitters, or sensory signals. Arrestin beta 1 is a cytosolic protein and acts as a cofactor in the beta-adrenergic receptor kinase (BARK) mediated desensitization of beta-adrenergic receptors. Besides the central nervous system, it is expressed at high levels in peripheral blood leukocytes, and thus the BARK/beta-arrestin system is believed to play a major role in regulating receptor-mediated immune functions. Alternatively spliced transcripts encoding different isoforms of arrestin beta 1 have been described. [provided by RefSeq, Jan 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARRB1	NM_004041.5	c.21-19296A>G		intron_variant	Intron 1 of 15	ENST00000420843.7	NP_004032.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARRB1	ENST00000420843.7	c.21-19296A>G		intron_variant	Intron 1 of 15	1	NM_004041.5	ENSP00000409581.2

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97806 AN: 152126 Hom.: 32129 Cov.: 36

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.643 AC: 97852 AN: 152246 Hom.: 32141 Cov.: 36 AF XY: 0.645 AC XY: 47992 AN XY: 74432

African (AFR) AF: 0.509 AC: 21124 AN: 41538

American (AMR) AF: 0.698 AC: 10679 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2258 AN: 3472

East Asian (EAS) AF: 0.484 AC: 2502 AN: 5166

South Asian (SAS) AF: 0.654 AC: 3162 AN: 4832

European-Finnish (FIN) AF: 0.717 AC: 7604 AN: 10612

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48222 AN: 67996

Other (OTH) AF: 0.641 AC: 1356 AN: 2116

Alfa AF: 0.688 Hom.: 54779

Bravo AF: 0.637

Asia WGS AF: 0.588 AC: 2042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.64
PhyloP100		-2.1
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: rs657561; hg19: chr11-75020379;