rs142323886
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_004985.5(KRAS):c.*3683delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000688 in 206,488 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000074 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0023 ( 0 hom. )
Consequence
KRAS
NM_004985.5 3_prime_UTR
NM_004985.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.614
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 -8 ACMG points.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0000739 (11/148814) while in subpopulation NFE AF= 0.000135 (9/66800). AF 95% confidence interval is 0.0000702. There are 0 homozygotes in gnomad4. There are 6 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 11 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRAS | NM_004985.5 | c.*3683delT | 3_prime_UTR_variant | Exon 5 of 5 | ENST00000311936.8 | NP_004976.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000672 AC: 10AN: 148708Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 0.00227 AC: 131AN: 57674Hom.: 0 Cov.: 0 AF XY: 0.00199 AC XY: 53AN XY: 26678
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GnomAD4 genome AF: 0.0000739 AC: 11AN: 148814Hom.: 0 Cov.: 31 AF XY: 0.0000828 AC XY: 6AN XY: 72490
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ClinVar
Not reported inComputational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at