2-206765635-T-G
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001136193.2(FASTKD2):c.-163T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000138 in 695,548 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00052 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000031 ( 0 hom. )
Consequence
FASTKD2
NM_001136193.2 5_prime_UTR
NM_001136193.2 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.26
Genes affected
FASTKD2 (HGNC:29160): (FAST kinase domains 2) This gene encodes a protein that is localized in the mitochondrial inner compartment and that may play a role in mitochondrial apoptosis. Nonsense mutations have been reported to result in cytochrome c oxidase deficiency. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 2-206765635-T-G is Benign according to our data. Variant chr2-206765635-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 380988.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FASTKD2 | NM_001136193.2 | c.-163T>G | 5_prime_UTR_variant | 1/12 | ENST00000402774.8 | NP_001129665.1 | ||
FASTKD2 | NM_001136194.2 | c.-178T>G | 5_prime_UTR_variant | 1/12 | NP_001129666.1 | |||
FASTKD2 | NM_014929.4 | c.-70T>G | 5_prime_UTR_variant | 1/12 | NP_055744.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FASTKD2 | ENST00000402774.8 | c.-163T>G | 5_prime_UTR_variant | 1/12 | 1 | NM_001136193.2 | ENSP00000385990 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000526 AC: 80AN: 152190Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.0000313 AC: 17AN: 543240Hom.: 0 Cov.: 8 AF XY: 0.0000272 AC XY: 7AN XY: 256982
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GnomAD4 genome AF: 0.000519 AC: 79AN: 152308Hom.: 0 Cov.: 31 AF XY: 0.000456 AC XY: 34AN XY: 74484
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 22, 2015 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at