19-55078089-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_133180.3(EPS8L1):c.19C>T(p.Pro7Ser) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000203 in 1,613,740 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict 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 Uncertain significance (★).
Frequency
Consequence
NM_133180.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152112Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250938Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135734
GnomAD4 exome AF: 0.000217 AC: 317AN: 1461628Hom.: 1 Cov.: 31 AF XY: 0.000227 AC XY: 165AN XY: 727102
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152112Hom.: 0 Cov.: 30 AF XY: 0.0000673 AC XY: 5AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.19C>T (p.P7S) alteration is located in exon 3 (coding exon 2) of the EPS8L1 gene. This alteration results from a C to T substitution at nucleotide position 19, causing the proline (P) at amino acid position 7 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at