chr1-1535428-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001114748.2(TMEM240):c.453C>T(p.Ala151=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00594 in 1,549,496 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0070 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0058 ( 45 hom. )
Consequence
TMEM240
NM_001114748.2 synonymous
NM_001114748.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.293
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
Variant 1-1535428-G-A is Benign according to our data. Variant chr1-1535428-G-A is described in ClinVar as [Benign]. Clinvar id is 593226.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-1535428-G-A is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=-0.293 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00704 (1070/152076) while in subpopulation AFR AF= 0.00892 (370/41476). AF 95% confidence interval is 0.00817. There are 2 homozygotes in gnomad4. There are 507 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1070 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM240 | NM_001114748.2 | c.453C>T | p.Ala151= | synonymous_variant | 4/4 | ENST00000378733.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM240 | ENST00000378733.9 | c.453C>T | p.Ala151= | synonymous_variant | 4/4 | 2 | NM_001114748.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00704 AC: 1070AN: 151968Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00416 AC: 615AN: 147878Hom.: 2 AF XY: 0.00423 AC XY: 334AN XY: 78988
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GnomAD4 exome AF: 0.00583 AC: 8141AN: 1397420Hom.: 45 Cov.: 33 AF XY: 0.00572 AC XY: 3944AN XY: 689260
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GnomAD4 genome ? AF: 0.00704 AC: 1070AN: 152076Hom.: 2 Cov.: 32 AF XY: 0.00682 AC XY: 507AN XY: 74342
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 08, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | TMEM240: BP4, BP7, BS1, BS2 - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 01, 2017 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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