2-206765747-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001136193.2(FASTKD2):c.-51A>G variant causes a splice region, 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00914 in 159,928 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001136193.2 splice_region, 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FASTKD2 | NM_001136193.2 | c.-51A>G | splice_region_variant, 5_prime_UTR_variant | 1/12 | ENST00000402774.8 | NP_001129665.1 | ||
FASTKD2 | NM_001136194.2 | c.-66A>G | 5_prime_UTR_variant | 1/12 | NP_001129666.1 | |||
FASTKD2 | NM_014929.4 | c.-51+93A>G | intron_variant | NP_055744.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FASTKD2 | ENST00000402774.8 | c.-51A>G | splice_region_variant, 5_prime_UTR_variant | 1/12 | 1 | NM_001136193.2 | ENSP00000385990 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00892 AC: 1357AN: 152102Hom.: 11 Cov.: 31
GnomAD4 exome AF: 0.0139 AC: 107AN: 7708Hom.: 2 Cov.: 4 AF XY: 0.0139 AC XY: 54AN XY: 3876
GnomAD4 genome AF: 0.00890 AC: 1355AN: 152220Hom.: 11 Cov.: 31 AF XY: 0.00981 AC XY: 730AN XY: 74420
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 21, 2013 | 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. - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 23, 2017 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 06, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | FASTKD2: BS1, BS2 - |
Combined oxidative phosphorylation deficiency 44 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 29, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at