chr3-4670829-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP4_StrongBP6
The NM_001378452.1(ITPR1):c.2107G>A(p.Asp703Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000036 in 1,610,944 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. D703D) has been classified as Likely benign.
Frequency
Consequence
NM_001378452.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITPR1 | NM_001378452.1 | c.2107G>A | p.Asp703Asn | missense_variant | 20/62 | ENST00000649015.2 | |
ITPR1 | NM_001168272.2 | c.2062G>A | p.Asp688Asn | missense_variant | 19/61 | ||
ITPR1 | NM_001099952.4 | c.2107G>A | p.Asp703Asn | missense_variant | 20/59 | ||
ITPR1 | NM_002222.7 | c.2062G>A | p.Asp688Asn | missense_variant | 19/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPR1 | ENST00000649015.2 | c.2107G>A | p.Asp703Asn | missense_variant | 20/62 | NM_001378452.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000820 AC: 20AN: 243822Hom.: 0 AF XY: 0.0000530 AC XY: 7AN XY: 132074
GnomAD4 exome AF: 0.0000343 AC: 50AN: 1458636Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 725236
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74486
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 23, 2018 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jul 11, 2022 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.2062G>A (p.D688N) alteration is located in exon 19 (coding exon 17) of the ITPR1 gene. This alteration results from a G to A substitution at nucleotide position 2062, causing the aspartic acid (D) at amino acid position 688 to be replaced by an asparagine (N). 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