11-77891764-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033547.4(INTS4):āc.2365A>Gā(p.Thr789Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,611,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_033547.4 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 |
---|---|---|---|---|---|---|---|
INTS4 | NM_033547.4 | c.2365A>G | p.Thr789Ala | missense_variant | 20/23 | ENST00000534064.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INTS4 | ENST00000534064.6 | c.2365A>G | p.Thr789Ala | missense_variant | 20/23 | 1 | NM_033547.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 247364Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134262
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1459712Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726162
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.2365A>G (p.T789A) alteration is located in exon 20 (coding exon 20) of the INTS4 gene. This alteration results from a A to G substitution at nucleotide position 2365, causing the threonine (T) at amino acid position 789 to be replaced by an alanine (A). 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