7-31578105-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001257967.3(ITPRID1):c.841G>A(p.Asp281Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,613,624 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001257967.3 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 |
---|---|---|---|---|---|---|---|
ITPRID1 | NM_001257967.3 | c.841G>A | p.Asp281Asn | missense_variant | 9/15 | ENST00000615280.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPRID1 | ENST00000615280.5 | c.841G>A | p.Asp281Asn | missense_variant | 9/15 | 2 | NM_001257967.3 | P2 | |
ITPRID1 | ENST00000407970.7 | c.841G>A | p.Asp281Asn | missense_variant | 8/14 | 1 | P2 | ||
ITPRID1 | ENST00000409210.1 | c.565G>A | p.Asp189Asn | missense_variant | 6/13 | 2 | A2 | ||
ITPRID1 | ENST00000319386.7 | c.726+115G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249502Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135048
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461460Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 726986
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at