rs121909251
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_198219.3(ING1):c.647A>G(p.Asn216Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
ING1
NM_198219.3 missense
NM_198219.3 missense
Scores
2
7
8
Clinical Significance
Conservation
PhyloP100: 6.94
Genes affected
ING1 (HGNC:6062): (inhibitor of growth family member 1) This gene encodes a tumor suppressor protein that can induce cell growth arrest and apoptosis. The encoded protein is a nuclear protein that physically interacts with the tumor suppressor protein TP53 and is a component of the p53 signaling pathway. Reduced expression and rearrangement of this gene have been detected in various cancers. Multiple alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 13-110719739-A-G is Pathogenic according to our data. Variant chr13-110719739-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 8068.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ING1 | NM_198219.3 | c.647A>G | p.Asn216Ser | missense_variant | 2/2 | ENST00000333219.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ING1 | ENST00000333219.9 | c.647A>G | p.Asn216Ser | missense_variant | 2/2 | 1 | NM_198219.3 | P1 | |
ING1 | ENST00000375774.3 | c.1076A>G | p.Asn359Ser | missense_variant | 2/2 | 1 | |||
ING1 | ENST00000338450.7 | c.515A>G | p.Asn172Ser | missense_variant | 2/2 | 1 | |||
ING1 | ENST00000375775.4 | c.440A>G | p.Asn147Ser | missense_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Squamous cell carcinoma of the head and neck Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 15, 2000 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T
M_CAP
Benign
D
MetaRNN
Uncertain
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D
REVEL
Uncertain
Sift
Uncertain
D;D;D;D
Sift4G
Benign
T;T;T;D
Polyphen
D;.;.;.
Vest4
MutPred
0.55
.;.;.;Gain of catalytic residue at S362 (P = 0);
MVP
MPC
1.8
ClinPred
D
GERP RS
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at