chr1-153728690-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_023015.5(INTS3):c.56C>T(p.Ala19Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000249 in 1,604,670 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_023015.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INTS3 | NM_023015.5 | c.56C>T | p.Ala19Val | missense_variant | 1/30 | ENST00000318967.7 | |
INTS3 | NM_001324475.2 | c.56C>T | p.Ala19Val | missense_variant | 2/31 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INTS3 | ENST00000318967.7 | c.56C>T | p.Ala19Val | missense_variant | 1/30 | 1 | NM_023015.5 | P1 | |
INTS3 | ENST00000435409.6 | c.56C>T | p.Ala19Val | missense_variant | 2/31 | 2 | P1 | ||
INTS3 | ENST00000481797.5 | n.208C>T | non_coding_transcript_exon_variant | 1/29 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 151978Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000831 AC: 2AN: 240738Hom.: 0 AF XY: 0.00000761 AC XY: 1AN XY: 131362
GnomAD4 exome AF: 6.88e-7 AC: 1AN: 1452692Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 723110
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 151978Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74230
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2023 | The c.56C>T (p.A19V) alteration is located in exon 1 (coding exon 1) of the INTS3 gene. This alteration results from a C to T substitution at nucleotide position 56, causing the alanine (A) at amino acid position 19 to be replaced by a valine (V). 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