chr18-751739-T-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005433.4(YES1):āc.337A>Cā(p.Lys113Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00634 in 1,601,440 control chromosomes in the GnomAD database, including 53 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0057 ( 6 hom., cov: 32)
Exomes š: 0.0064 ( 47 hom. )
Consequence
YES1
NM_005433.4 missense
NM_005433.4 missense
Scores
1
4
8
Clinical Significance
Conservation
PhyloP100: 7.91
Genes affected
YES1 (HGNC:12841): (YES proto-oncogene 1, Src family tyrosine kinase) This gene is the cellular homolog of the Yamaguchi sarcoma virus oncogene. The encoded protein has tyrosine kinase activity and belongs to the src family of proteins. This gene lies in close proximity to thymidylate synthase gene on chromosome 18, and a corresponding pseudogene has been found on chromosome 22. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.009892702).
BP6
Variant 18-751739-T-G is Benign according to our data. Variant chr18-751739-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 2648515.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 875 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YES1 | NM_005433.4 | c.337A>C | p.Lys113Gln | missense_variant | 3/12 | ENST00000314574.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YES1 | ENST00000314574.5 | c.337A>C | p.Lys113Gln | missense_variant | 3/12 | 1 | NM_005433.4 | P1 | |
YES1 | ENST00000584307.5 | c.337A>C | p.Lys113Gln | missense_variant | 3/12 | 1 | P1 | ||
YES1 | ENST00000577961.5 | c.352A>C | p.Lys118Gln | missense_variant | 3/12 | 5 | |||
YES1 | ENST00000577611.1 | n.553A>C | non_coding_transcript_exon_variant | 4/4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00575 AC: 875AN: 152164Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00550 AC: 1381AN: 250892Hom.: 6 AF XY: 0.00544 AC XY: 738AN XY: 135668
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GnomAD4 exome AF: 0.00641 AC: 9282AN: 1449158Hom.: 47 Cov.: 28 AF XY: 0.00629 AC XY: 4540AN XY: 721710
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GnomAD4 genome AF: 0.00575 AC: 875AN: 152282Hom.: 6 Cov.: 32 AF XY: 0.00628 AC XY: 468AN XY: 74478
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2023 | YES1: BS2 - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;.;D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
Sift4G
Benign
T;T;T
Polyphen
0.0010
.;B;B
Vest4
MVP
MPC
0.35
ClinPred
T
GERP RS
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at