chr17-50375405-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152463.4(EME1):c.197C>T(p.Pro66Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000719 in 1,614,180 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P66A) has been classified as Uncertain significance.
Frequency
Consequence
NM_152463.4 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: 0.000414 AC: 63AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251460Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135908
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461888Hom.: 0 Cov.: 29 AF XY: 0.0000330 AC XY: 24AN XY: 727246
GnomAD4 genome AF: 0.000414 AC: 63AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.000362 AC XY: 27AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.197C>T (p.P66L) alteration is located in exon 2 (coding exon 1) of the EME1 gene. This alteration results from a C to T substitution at nucleotide position 197, causing the proline (P) at amino acid position 66 to be replaced by a leucine (L). 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