11-77907739-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033547.4(INTS4):c.1994G>A(p.Arg665His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,120 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033547.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INTS4 | NM_033547.4 | c.1994G>A | p.Arg665His | missense_variant | 16/23 | ENST00000534064.6 | |
INTS4 | XM_017018560.3 | c.1994G>A | p.Arg665His | missense_variant | 16/23 | ||
INTS4 | XR_001748036.3 | n.2019G>A | non_coding_transcript_exon_variant | 16/21 | |||
INTS4 | XR_002957208.2 | n.2019G>A | non_coding_transcript_exon_variant | 16/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INTS4 | ENST00000534064.6 | c.1994G>A | p.Arg665His | missense_variant | 16/23 | 1 | NM_033547.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250812Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135570
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461046Hom.: 0 Cov.: 29 AF XY: 0.0000110 AC XY: 8AN XY: 726858
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 05, 2022 | The c.1994G>A (p.R665H) alteration is located in exon 16 (coding exon 16) of the INTS4 gene. This alteration results from a G to A substitution at nucleotide position 1994, causing the arginine (R) at amino acid position 665 to be replaced by a histidine (H). 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