2-119437097-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_183240.3(TMEM37):c.230G>A(p.Gly77Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00523 in 1,614,008 control chromosomes in the GnomAD database, including 262 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.024 ( 131 hom., cov: 34)
Exomes 𝑓: 0.0032 ( 131 hom. )
Consequence
TMEM37
NM_183240.3 missense
NM_183240.3 missense
Scores
16
Clinical Significance
Conservation
PhyloP100: 0.363
Genes affected
TMEM37 (HGNC:18216): (transmembrane protein 37) Predicted to enable calcium channel activity and voltage-gated ion channel activity. Predicted to be involved in calcium ion transmembrane transport and regulation of ion transmembrane transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0022252202).
BP6
?
Variant 2-119437097-G-A is Benign according to our data. Variant chr2-119437097-G-A is described in ClinVar as [Benign]. Clinvar id is 780835.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0776 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM37 | NM_183240.3 | c.230G>A | p.Gly77Asp | missense_variant | 2/2 | ENST00000306406.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM37 | ENST00000306406.5 | c.230G>A | p.Gly77Asp | missense_variant | 2/2 | 1 | NM_183240.3 | P2 | |
TMEM37 | ENST00000409826.1 | c.266G>A | p.Gly89Asp | missense_variant | 2/2 | 3 | A2 | ||
TMEM37 | ENST00000465296.1 | n.370G>A | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
TMEM37 | ENST00000417645.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0242 AC: 3678AN: 152090Hom.: 128 Cov.: 34
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00705 AC: 1768AN: 250804Hom.: 56 AF XY: 0.00546 AC XY: 741AN XY: 135594
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GnomAD4 exome AF: 0.00325 AC: 4744AN: 1461800Hom.: 131 Cov.: 35 AF XY: 0.00291 AC XY: 2117AN XY: 727198
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GnomAD4 genome ? AF: 0.0243 AC: 3692AN: 152208Hom.: 131 Cov.: 34 AF XY: 0.0229 AC XY: 1707AN XY: 74416
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995
Asia WGS
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18
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 14, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
0.058
.;B
Vest4
MVP
MPC
0.54
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at