chr13-110715912-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000375774.3(ING1):c.469T>C(p.Ser157Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,576,422 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000375774.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ING1 | NM_198219.3 | c.136+1627T>C | intron_variant | ENST00000333219.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ING1 | ENST00000333219.9 | c.136+1627T>C | intron_variant | 1 | NM_198219.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152210Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000338 AC: 7AN: 206966Hom.: 0 AF XY: 0.0000258 AC XY: 3AN XY: 116400
GnomAD4 exome AF: 0.0000246 AC: 35AN: 1424212Hom.: 0 Cov.: 51 AF XY: 0.0000170 AC XY: 12AN XY: 707188
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152210Hom.: 0 Cov.: 34 AF XY: 0.0000538 AC XY: 4AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 01, 2023 | The c.469T>C (p.S157P) alteration is located in exon 1 (coding exon 1) of the ING1 gene. This alteration results from a T to C substitution at nucleotide position 469, causing the serine (S) at amino acid position 157 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at