chr1-1535276-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001114748.2(TMEM240):c.*83C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000706 in 1,472,224 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0035 ( 3 hom., cov: 31)
Exomes 𝑓: 0.00038 ( 3 hom. )
Consequence
TMEM240
NM_001114748.2 3_prime_UTR
NM_001114748.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.244
Genes affected
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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 (BayesDel_noAF=-0.92).
BP6
?
Variant 1-1535276-G-A is Benign according to our data. Variant chr1-1535276-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1702646.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00352 (534/151818) while in subpopulation AFR AF= 0.0123 (507/41374). AF 95% confidence interval is 0.0114. There are 3 homozygotes in gnomad4. There are 249 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 535 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM240 | NM_001114748.2 | c.*83C>T | 3_prime_UTR_variant | 4/4 | ENST00000378733.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM240 | ENST00000378733.9 | c.*83C>T | 3_prime_UTR_variant | 4/4 | 2 | NM_001114748.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00353 AC: 535AN: 151706Hom.: 3 Cov.: 31
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GnomAD4 exome AF: 0.000383 AC: 506AN: 1320406Hom.: 3 Cov.: 27 AF XY: 0.000385 AC XY: 249AN XY: 646898
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GnomAD4 genome ? AF: 0.00352 AC: 534AN: 151818Hom.: 3 Cov.: 31 AF XY: 0.00336 AC XY: 249AN XY: 74180
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 18, 2022 | See Variant Classification Assertion Criteria. - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at