Menu
GeneBe

rs3733890

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001713(BHMT):c.716G>A(p.Arg239Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151846 control chromosomes in the gnomAD Genomes database, including 5975 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 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 Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.28 ( 5975 hom., cov: 31)
Exomes 𝑓: 0.30 ( 11846 hom. )

Consequence

BHMT
NM_001713 missense

Scores

2
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.86

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (MetaRNN=0.0020504296).
BA1
?
GnomAd highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BHMTNM_001713.3 linkuse as main transcriptc.716G>A p.Arg239Gln missense_variant 6/8 ENST00000274353.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BHMTENST00000274353.10 linkuse as main transcriptc.716G>A p.Arg239Gln missense_variant 6/81 NM_001713.3 P1

Frequencies

GnomAD3 genomes
AF:
0.277
AC:
42017
AN:
151846
Hom.:
5975
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.221
Gnomad AMI
AF:
0.254
Gnomad AMR
AF:
0.341
Gnomad ASJ
AF:
0.319
Gnomad EAS
AF:
0.317
Gnomad SAS
AF:
0.280
Gnomad FIN
AF:
0.240
Gnomad MID
AF:
0.294
Gnomad NFE
AF:
0.296
Gnomad OTH
AF:
0.305
GnomAD3 exomes
AF:
0.302
AC:
75970
AN:
251278
Hom.:
11846
AF XY:
0.302
AC XY:
41045
AN XY:
135816
show subpopulations
Gnomad AFR exome
AF:
0.222
Gnomad AMR exome
AF:
0.382
Gnomad ASJ exome
AF:
0.340
Gnomad EAS exome
AF:
0.324
Gnomad SAS exome
AF:
0.289
Gnomad FIN exome
AF:
0.241
Gnomad NFE exome
AF:
0.298
Gnomad OTH exome
AF:
0.310
GnomAD4 exome
AF:
0.293
AC:
427841
AN:
1460856
Hom.:
63643
AF XY:
0.293
AC XY:
212945
AN XY:
726532
show subpopulations
Gnomad4 AFR exome
AF:
0.220
Gnomad4 AMR exome
AF:
0.378
Gnomad4 ASJ exome
AF:
0.336
Gnomad4 EAS exome
AF:
0.271
Gnomad4 SAS exome
AF:
0.286
Gnomad4 FIN exome
AF:
0.244
Gnomad4 NFE exome
AF:
0.294
Gnomad4 OTH exome
AF:
0.288
Alfa
AF:
0.302
Hom.:
14962
Bravo
AF:
0.285
TwinsUK
AF:
0.309
AC:
1144
ALSPAC
AF:
0.300
AC:
1155
ESP6500AA
AF:
0.222
AC:
980
ESP6500EA
AF:
0.300
AC:
2584
ExAC
AF:
0.295
AC:
35825
Asia WGS
AF:
0.273
AC:
947
AN:
3478
EpiCase
AF:
0.312
EpiControl
AF:
0.312

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.075
BayesDel_addAF
Benign
-0.71
T
BayesDel_noAF
Benign
-0.65
Cadd
Benign
22
Dann
Uncertain
1.0
DEOGEN2
Benign
0.074
T;T
Eigen
Benign
-0.54
Eigen_PC
Benign
-0.47
FATHMM_MKL
Benign
0.22
N
LIST_S2
Benign
0.16
T;T
MetaRNN
Benign
0.0021
T;T
MetaSVM
Benign
-0.94
T
MutationAssessor
Benign
1.4
L;.
MutationTaster
Benign
1.0
P;P
PrimateAI
Benign
0.24
T
PROVEAN
Benign
-0.16
N;N
REVEL
Benign
0.058
Sift
Benign
0.051
T;T
Sift4G
Uncertain
0.022
D;D
Polyphen
0.0
B;P
Vest4
0.084
MPC
0.11
ClinPred
0.011
T
GERP RS
3.5
Varity_R
0.058
gMVP
0.54

Splicing

Find out detailed SpliceAI scores 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: rs3733890; hg19: chr5-78421959; COSMIC: COSV57153716;