GeneBe

rs1346352608

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001385089.1(BEGAIN):​c.1630G>C​(p.Gly544Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 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 the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

Frequency

Genomes: not found (cov: 33)

Consequence

BEGAIN
NM_001385089.1 missense

Scores

1
1
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00100

Publications

1 publications found
Variant links:
Genes affected
BEGAIN (HGNC:24163): (brain enriched guanylate kinase associated) Predicted to be involved in regulation of postsynaptic neurotransmitter receptor activity. Predicted to act upstream of or within evoked excitatory postsynaptic potential. Predicted to be located in dendrite; nucleus; and presynapse. Predicted to be active in glutamatergic synapse and postsynapse. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.101567626).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001385089.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
BEGAIN
NM_001385089.1
MANE Select
c.1630G>Cp.Gly544Arg
missense
Exon 7 of 7NP_001372018.1G3V3A2
BEGAIN
NM_001385085.1
c.1720G>Cp.Gly574Arg
missense
Exon 8 of 8NP_001372014.1
BEGAIN
NM_001385086.1
c.1702G>Cp.Gly568Arg
missense
Exon 8 of 8NP_001372015.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
BEGAIN
ENST00000554140.3
TSL:5 MANE Select
c.1630G>Cp.Gly544Arg
missense
Exon 7 of 7ENSP00000451125.2G3V3A2
BEGAIN
ENST00000355173.7
TSL:1
c.1573G>Cp.Gly525Arg
missense
Exon 7 of 7ENSP00000347301.2Q9BUH8
BEGAIN
ENST00000557378.6
TSL:1
c.1573G>Cp.Gly525Arg
missense
Exon 6 of 6ENSP00000450722.2Q9BUH8

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD2 exomes
AF:
0.00
AC:
0
AN:
137856
AF XY:
0.00
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.26
T
BayesDel_noAF
Benign
-0.61
CADD
Benign
9.2
DANN
Benign
0.95
DEOGEN2
Benign
0.017
T
Eigen
Benign
-0.78
Eigen_PC
Benign
-0.76
FATHMM_MKL
Benign
0.22
N
LIST_S2
Benign
0.81
T
M_CAP
Uncertain
0.12
D
MetaRNN
Benign
0.10
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.49
N
PhyloP100
0.0010
PrimateAI
Pathogenic
0.86
D
PROVEAN
Benign
-1.1
N
REVEL
Benign
0.022
Sift
Benign
0.16
T
Sift4G
Benign
0.38
T
Polyphen
0.0030
B
Vest4
0.080
MutPred
0.37
Gain of catalytic residue at G521 (P = 0.0029)
MVP
0.068
MPC
0.52
ClinPred
0.031
T
GERP RS
0.82
Varity_R
0.072
gMVP
0.13
Mutation Taster
=95/5
polymorphism

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

Publications

Other links and lift over

dbSNP: rs1346352608; hg19: chr14-101004515; API