12-25207290-A-G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_004985.5(KRAS):c.*2505T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
KRAS
NM_004985.5 3_prime_UTR
NM_004985.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.836
Publications
135 publications found
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 was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_004985.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| KRAS | TSL:1 MANE Plus Clinical | c.*2626T>C | 3_prime_UTR | Exon 6 of 6 | ENSP00000256078.5 | P01116-1 | |||
| KRAS | TSL:1 MANE Select | c.*2505T>C | 3_prime_UTR | Exon 5 of 5 | ENSP00000308495.3 | P01116-2 | |||
| KRAS | c.*2505T>C | 3_prime_UTR | Exon 5 of 5 | ENSP00000508921.1 | P01116-2 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 152108Hom.: 0 Cov.: 31
GnomAD3 genomes
AF:
AC:
0
AN:
152108
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
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Gnomad NFE
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Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 43756Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 20400
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
43756
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
20400
African (AFR)
AF:
AC:
0
AN:
1792
American (AMR)
AF:
AC:
0
AN:
1206
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2818
East Asian (EAS)
AF:
AC:
0
AN:
7304
South Asian (SAS)
AF:
AC:
0
AN:
354
European-Finnish (FIN)
AF:
AC:
0
AN:
24
Middle Eastern (MID)
AF:
AC:
0
AN:
288
European-Non Finnish (NFE)
AF:
AC:
0
AN:
26306
Other (OTH)
AF:
AC:
0
AN:
3664
GnomAD4 genome 0.00 AC: 0AN: 152108Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74304
GnomAD4 genome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
152108
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
74304
African (AFR)
AF:
AC:
0
AN:
41418
American (AMR)
AF:
AC:
0
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5186
South Asian (SAS)
AF:
AC:
0
AN:
4826
European-Finnish (FIN)
AF:
AC:
0
AN:
10608
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68022
Other (OTH)
AF:
AC:
0
AN:
2084
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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