1-153728654-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_023015.5(INTS3):āc.20A>Gā(p.Lys7Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000747 in 1,605,640 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_023015.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INTS3 | NM_023015.5 | c.20A>G | p.Lys7Arg | missense_variant | 1/30 | ENST00000318967.7 | |
INTS3 | NM_001324475.2 | c.20A>G | p.Lys7Arg | missense_variant | 2/31 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INTS3 | ENST00000318967.7 | c.20A>G | p.Lys7Arg | missense_variant | 1/30 | 1 | NM_023015.5 | P1 | |
INTS3 | ENST00000435409.6 | c.20A>G | p.Lys7Arg | missense_variant | 2/31 | 2 | P1 | ||
INTS3 | ENST00000481797.5 | n.172A>G | non_coding_transcript_exon_variant | 1/29 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000724 AC: 11AN: 152038Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000374 AC: 9AN: 240754Hom.: 0 AF XY: 0.0000228 AC XY: 3AN XY: 131542
GnomAD4 exome AF: 0.0000750 AC: 109AN: 1453602Hom.: 0 Cov.: 32 AF XY: 0.0000857 AC XY: 62AN XY: 723488
GnomAD4 genome AF: 0.0000724 AC: 11AN: 152038Hom.: 0 Cov.: 30 AF XY: 0.0000539 AC XY: 4AN XY: 74264
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2021 | The c.20A>G (p.K7R) alteration is located in exon 1 (coding exon 1) of the INTS3 gene. This alteration results from a A to G substitution at nucleotide position 20, causing the lysine (K) at amino acid position 7 to be replaced by an arginine (R). 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