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GeneBe

rs1801253

chr10-114045297-G-Achr10-114045297-G-C

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM2_SupportingBP4_Strong

The NM_000684(ADRB1):c.1165G>A(p.Gly389Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD Genomes project. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G389V) has been classified as Benign.

Frequency

Genomes: not found (cov: 34)

Consequence

ADRB1
NM_000684 missense

Scores

1
1
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.04

Links

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 34.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.059390485).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ADRB1NM_000684.3 linkuse as main transcriptc.1165G>A p.Gly389Arg missense_variant 1/1 ENST00000369295.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ADRB1ENST00000369295.4 linkuse as main transcriptc.1165G>A p.Gly389Arg missense_variant 1/1 NM_000684.3 P1

Frequencies

GnomAD3 genomes
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.081
BayesDel_addAF
Benign
-0.31
T
BayesDel_noAF
Benign
-0.68
Cadd
Benign
17
Dann
Benign
0.96
Eigen
Benign
-0.49
Eigen_PC
Benign
-0.49
FATHMM_MKL
Benign
0.28
N
M_CAP
Uncertain
0.11
D
MetaRNN
Benign
0.059
T
MetaSVM
Benign
-0.97
T
MutationTaster
Benign
1.0
N
PrimateAI
Pathogenic
0.89
D
PROVEAN
Benign
3.2
N
REVEL
Benign
0.071
Sift
Benign
1.0
T
Sift4G
Benign
1.0
T
Vest4
0.055
MutPred
0.32
Gain of MoRF binding (P = 0.02);
MVP
0.51
ClinPred
0.48
T
GERP RS
1.7
gMVP
0.54

Splicing

Find out SpliceAI 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: rs1801253; hg19: chr10-115805056;