rs397517040
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PP5_ModerateBP4BP7
The NM_004985.5(KRAS):c.39C>T(p.Gly13=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,460,512 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. G13G) has been classified as Likely pathogenic.
Frequency
Consequence
NM_004985.5 synonymous
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 | UniProt |
---|---|---|---|---|---|---|---|
KRAS | NM_033360.4 | c.39C>T | p.Gly13= | synonymous_variant | 2/6 | ENST00000256078.10 | |
KRAS | NM_004985.5 | c.39C>T | p.Gly13= | synonymous_variant | 2/5 | ENST00000311936.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRAS | ENST00000256078.10 | c.39C>T | p.Gly13= | synonymous_variant | 2/6 | 1 | NM_033360.4 | A1 | |
KRAS | ENST00000311936.8 | c.39C>T | p.Gly13= | synonymous_variant | 2/5 | 1 | NM_004985.5 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249446Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134796
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460512Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726488
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Non-small cell lung carcinoma Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Oct 12, 2011 | DNA sequencing of KRAS identified the variants listed above. From this test, we are unable to determine if these variants occur on the same chromosome (in cis) or on different chromosomes (in trans; as listed above). The Gly13Val variant h as been reported in 1 lung adenocarcinoma that did not respond to TKI treatment (Marchetti 2009; COSMIC). The Gly13Gly variant has not been reported in a lung t umor, but has been seen in several other tumor sites, including pancreas and lar ge intestine (COSMIC). If the two variants occur on the same chromosome (in cis) , the resulting variant would be 38_39delinsTT (Gly13Val), which has been previo usly identified in 2 lung carcinomas (COSMIC). Somatic KRAS variants have been a ssociated with resistance to EGFR TKIs (Pao 2005). - |
Prostate cancer, hereditary, 1 Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Laboratory of Virology, Oncology, Biosciences and Environment, Faculty of Sciences and Techniques, Mohammedia- University Hassan II of Casablanca | Jul 29, 2022 | - - |
not provided Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at