chr2-206766737-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001136193.2(FASTKD2):c.44G>A(p.Ser15Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0866 in 1,613,708 control chromosomes in the GnomAD database, including 7,451 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001136193.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.44G>A | p.Ser15Asn | missense_variant | 2/12 | ENST00000402774.8 | NP_001129665.1 | |
FASTKD2 | NM_001136194.2 | c.44G>A | p.Ser15Asn | missense_variant | 2/12 | NP_001129666.1 | ||
FASTKD2 | NM_014929.4 | c.44G>A | p.Ser15Asn | missense_variant | 2/12 | NP_055744.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FASTKD2 | ENST00000402774.8 | c.44G>A | p.Ser15Asn | missense_variant | 2/12 | 1 | NM_001136193.2 | ENSP00000385990 | P1 |
Frequencies
GnomAD3 genomes AF: 0.119 AC: 18123AN: 152078Hom.: 1528 Cov.: 33
GnomAD3 exomes AF: 0.0795 AC: 19976AN: 251196Hom.: 1140 AF XY: 0.0783 AC XY: 10635AN XY: 135794
GnomAD4 exome AF: 0.0832 AC: 121647AN: 1461510Hom.: 5912 Cov.: 32 AF XY: 0.0825 AC XY: 59991AN XY: 727064
GnomAD4 genome AF: 0.119 AC: 18171AN: 152198Hom.: 1539 Cov.: 33 AF XY: 0.116 AC XY: 8665AN XY: 74406
ClinVar
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 15, 2016 | - - |
Mitochondrial complex IV deficiency, nuclear type 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at