chr2-119437075-A-AGTGTGC
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_183240.3(TMEM37):c.208_209insGTGTGC(p.Thr70delinsSerValPro) variant causes a protein altering change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.866 in 1,613,660 control chromosomes in the GnomAD database, including 606,389 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.89 ( 60088 hom., cov: 0)
Exomes 𝑓: 0.86 ( 546301 hom. )
Consequence
TMEM37
NM_183240.3 protein_altering
NM_183240.3 protein_altering
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.00
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 -10 ACMG points.
BP6
?
Variant 2-119437075-A-AGTGTGC is Benign according to our data. Variant chr2-119437075-A-AGTGTGC is described in ClinVar as [Benign]. Clinvar id is 767819.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM37 | NM_183240.3 | c.208_209insGTGTGC | p.Thr70delinsSerValPro | protein_altering_variant | 2/2 | ENST00000306406.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM37 | ENST00000306406.5 | c.208_209insGTGTGC | p.Thr70delinsSerValPro | protein_altering_variant | 2/2 | 1 | NM_183240.3 | P2 | |
TMEM37 | ENST00000409826.1 | c.244_245insGTGTGC | p.Thr82delinsSerValPro | protein_altering_variant | 2/2 | 3 | A2 | ||
TMEM37 | ENST00000465296.1 | n.348_349insGTGTGC | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
TMEM37 | ENST00000417645.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.888 AC: 134752AN: 151698Hom.: 60032 Cov.: 0
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GnomAD3 exomes AF: 0.858 AC: 215387AN: 250980Hom.: 92732 AF XY: 0.860 AC XY: 116678AN XY: 135678
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GnomAD4 exome AF: 0.864 AC: 1263225AN: 1461844Hom.: 546301 Cov.: 33 AF XY: 0.864 AC XY: 628405AN XY: 727224
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GnomAD4 genome ? AF: 0.888 AC: 134871AN: 151816Hom.: 60088 Cov.: 0 AF XY: 0.885 AC XY: 65647AN XY: 74188
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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 | Dec 31, 2019 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at