7-31578000-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001257967.3(ITPRID1):c.736G>A(p.Ala246Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000564 in 1,613,618 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 Likely benign (★).
Frequency
Consequence
NM_001257967.3 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 |
---|---|---|---|---|---|---|---|
ITPRID1 | NM_001257967.3 | c.736G>A | p.Ala246Thr | missense_variant | 9/15 | ENST00000615280.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPRID1 | ENST00000615280.5 | c.736G>A | p.Ala246Thr | missense_variant | 9/15 | 2 | NM_001257967.3 | P2 | |
ITPRID1 | ENST00000407970.7 | c.736G>A | p.Ala246Thr | missense_variant | 8/14 | 1 | P2 | ||
ITPRID1 | ENST00000409210.1 | c.460G>A | p.Ala154Thr | missense_variant | 6/13 | 2 | A2 | ||
ITPRID1 | ENST00000319386.7 | c.726+10G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000520 AC: 13AN: 250154Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135128
GnomAD4 exome AF: 0.0000534 AC: 78AN: 1461524Hom.: 0 Cov.: 30 AF XY: 0.0000468 AC XY: 34AN XY: 727022
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152094Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74292
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at