12-47718131-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000422538.8(ENDOU):c.242G>T(p.Ser81Ile) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000564 in 1,418,386 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 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
ENST00000422538.8 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ENDOU | NM_001172439.2 | c.242G>T | p.Ser81Ile | missense_variant, splice_region_variant | 3/10 | ENST00000422538.8 | NP_001165910.1 | |
RPAP3-DT | NR_183480.1 | n.77-1016C>A | intron_variant, non_coding_transcript_variant | |||||
ENDOU | NM_006025.4 | c.119G>T | p.Ser40Ile | missense_variant, splice_region_variant | 2/9 | NP_006016.1 | ||
ENDOU | NM_001172440.2 | c.56-476G>T | intron_variant | NP_001165911.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENDOU | ENST00000422538.8 | c.242G>T | p.Ser81Ile | missense_variant, splice_region_variant | 3/10 | 1 | NM_001172439.2 | ENSP00000397679 | P1 | |
RPAP3-DT | ENST00000547799.5 | n.224+495C>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000564 AC: 8AN: 1418386Hom.: 0 Cov.: 31 AF XY: 0.00000570 AC XY: 4AN XY: 701180
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 02, 2023 | The c.242G>T (p.S81I) alteration is located in exon 3 (coding exon 3) of the ENDOU gene. This alteration results from a G to T substitution at nucleotide position 242, causing the serine (S) at amino acid position 81 to be replaced by an isoleucine (I). 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