chr13-110715990-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000375774.3(ING1):c.547C>T(p.Arg183Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000166 in 1,505,240 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 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+1705C>T | intron_variant | ENST00000333219.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ING1 | ENST00000333219.9 | c.136+1705C>T | intron_variant | 1 | NM_198219.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000400 AC: 6AN: 150154Hom.: 0 AF XY: 0.0000479 AC XY: 4AN XY: 83456
GnomAD4 exome AF: 0.0000155 AC: 21AN: 1352898Hom.: 0 Cov.: 34 AF XY: 0.0000256 AC XY: 17AN XY: 664544
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152342Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.547C>T (p.R183C) alteration is located in exon 1 (coding exon 1) of the ING1 gene. This alteration results from a C to T substitution at nucleotide position 547, causing the arginine (R) at amino acid position 183 to be replaced by a cysteine (C). 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