18-751793-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_005433.4(YES1):c.283A>G(p.Ile95Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000145 in 1,588,622 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005433.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YES1 | NM_005433.4 | c.283A>G | p.Ile95Val | missense_variant | 3/12 | ENST00000314574.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YES1 | ENST00000314574.5 | c.283A>G | p.Ile95Val | missense_variant | 3/12 | 1 | NM_005433.4 | P1 | |
YES1 | ENST00000584307.5 | c.283A>G | p.Ile95Val | missense_variant | 3/12 | 1 | P1 | ||
YES1 | ENST00000577961.5 | c.298A>G | p.Ile100Val | missense_variant | 3/12 | 5 | |||
YES1 | ENST00000577611.1 | n.499A>G | non_coding_transcript_exon_variant | 4/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249370Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134972
GnomAD4 exome AF: 0.0000132 AC: 19AN: 1437374Hom.: 0 Cov.: 27 AF XY: 0.0000153 AC XY: 11AN XY: 716700
GnomAD4 genome ? AF: 0.0000264 AC: 4AN: 151248Hom.: 0 Cov.: 32 AF XY: 0.0000542 AC XY: 4AN XY: 73800
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.283A>G (p.I95V) alteration is located in exon 3 (coding exon 2) of the YES1 gene. This alteration results from a A to G substitution at nucleotide position 283, causing the isoleucine (I) at amino acid position 95 to be replaced by a valine (V). 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