chr8-11808804-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004462.5(FDFT1):c.110G>A(p.Ser37Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000793 in 1,613,538 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 Uncertain significance (no stars).
Frequency
Consequence
NM_004462.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000163 AC: 41AN: 250812Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135574
GnomAD4 exome AF: 0.0000842 AC: 123AN: 1461278Hom.: 0 Cov.: 43 AF XY: 0.000128 AC XY: 93AN XY: 726852
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152260Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74436
ClinVar
Submissions by phenotype
not provided Uncertain:1
The FDFT1 p.Ser37Asn variant was not identified in the literature nor was it identified in ClinVar or LOVD 3.0. The variant was identified in dbSNP (ID: rs558707651) and in control databases in 41 of 250812 chromosomes at a frequency of 0.0001635 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: South Asian in 38 of 30542 chromosomes (freq: 0.001244) and Other in 3 of 6132 chromosomes (freq: 0.000489), but was not observed in the African, Latino, Ashkenazi Jewish, East Asian, European (Finnish) or European (non-Finnish) populations. The p.Ser37 residue is conserved in mammals but not in more distantly related organisms however four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and three of four in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at