rs397517035
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_004985.5(KRAS):c.-178_-170delCGCGGCGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000797 in 251,066 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000086 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000071 ( 0 hom. )
Consequence
KRAS
NM_004985.5 5_prime_UTR
NM_004985.5 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.72
Genes affected
KRAS (HGNC:6407): (KRAS proto-oncogene, GTPase) This gene, a Kirsten ras oncogene homolog from the mammalian ras gene family, encodes a protein that is a member of the small GTPase superfamily. A single amino acid substitution is responsible for an activating mutation. The transforming protein that results is implicated in various malignancies, including lung adenocarcinoma, mucinous adenoma, ductal carcinoma of the pancreas and colorectal carcinoma. Alternative splicing leads to variants encoding two isoforms that differ in the C-terminal region. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 12-25250908-CGCCGCCGCG-C is Benign according to our data. Variant chr12-25250908-CGCCGCCGCG-C is described in ClinVar as [Benign]. Clinvar id is 45112.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0000855 (13/152032) while in subpopulation NFE AF= 0.000191 (13/67962). AF 95% confidence interval is 0.000112. There are 0 homozygotes in gnomad4. There are 6 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 13 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRAS | NM_004985.5 | c.-178_-170delCGCGGCGGC | 5_prime_UTR_variant | 1/5 | ENST00000311936.8 | NP_004976.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KRAS | ENST00000311936.8 | c.-178_-170delCGCGGCGGC | 5_prime_UTR_variant | 1/5 | 1 | NM_004985.5 | ENSP00000308495.3 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152032Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000707 AC: 7AN: 99034Hom.: 0 AF XY: 0.0000941 AC XY: 5AN XY: 53114
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GnomAD4 genome AF: 0.0000855 AC: 13AN: 152032Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74270
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 16, 2012 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at