chr1-171784473-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_015935.5(METTL13):c.887G>A(p.Arg296Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000292 in 1,505,246 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00053 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00027 ( 0 hom. )
Consequence
METTL13
NM_015935.5 missense
NM_015935.5 missense
Scores
1
4
12
Clinical Significance
Conservation
PhyloP100: 4.46
Genes affected
METTL13 (HGNC:24248): (methyltransferase 13, eEF1A N-terminus and K55) Predicted to enable methyltransferase activity. Involved in negative regulation of cell cycle G1/S phase transition and negative regulation of transcription by RNA polymerase II. Predicted to be located in mitochondrion and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0075309277).
BP6
?
Variant 1-171784473-G-A is Benign according to our data. Variant chr1-171784473-G-A is described in ClinVar as [Benign]. Clinvar id is 3050377.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 80 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
METTL13 | NM_015935.5 | c.887G>A | p.Arg296Gln | missense_variant | 2/8 | ENST00000361735.4 | |
METTL13 | NM_014955.3 | c.629G>A | p.Arg210Gln | missense_variant | 2/8 | ||
METTL13 | NM_001007239.2 | c.453+434G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
METTL13 | ENST00000361735.4 | c.887G>A | p.Arg296Gln | missense_variant | 2/8 | 1 | NM_015935.5 | P1 | |
METTL13 | ENST00000367737.9 | c.453+434G>A | intron_variant | 1 | |||||
METTL13 | ENST00000362019.7 | c.629G>A | p.Arg210Gln | missense_variant | 2/8 | 2 | |||
METTL13 | ENST00000485629.1 | n.565+434G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000526 AC: 80AN: 152222Hom.: 1 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
80
AN:
152222
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000341 AC: 56AN: 164062Hom.: 0 AF XY: 0.000341 AC XY: 30AN XY: 87884
GnomAD3 exomes
AF:
AC:
56
AN:
164062
Hom.:
AF XY:
AC XY:
30
AN XY:
87884
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000266 AC: 360AN: 1353024Hom.: 0 Cov.: 34 AF XY: 0.000256 AC XY: 169AN XY: 661188
GnomAD4 exome
AF:
AC:
360
AN:
1353024
Hom.:
Cov.:
34
AF XY:
AC XY:
169
AN XY:
661188
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000526 AC: 80AN: 152222Hom.: 1 Cov.: 33 AF XY: 0.000498 AC XY: 37AN XY: 74358
GnomAD4 genome
?
AF:
AC:
80
AN:
152222
Hom.:
Cov.:
33
AF XY:
AC XY:
37
AN XY:
74358
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ESP6500AA
AF:
AC:
0
ESP6500EA
AF:
AC:
7
ExAC
?
AF:
AC:
36
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
METTL13-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 11, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Pathogenic
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;D
Sift4G
Benign
T;T
Polyphen
0.88
.;P
Vest4
MVP
MPC
0.29
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at