rs750792790

Variant names:

• chr7-31553113-C-A
• rs750792790
• NM_001257967.3:c.89C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-31553113-C-A
• chr7-31553113-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001257967.3(ITPRID1):​c.89C>A​(p.Ala30Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ITPRID1 NM_001257967.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

Genes affected

ITPRID1 (HGNC:27363): (ITPR interacting domain containing 1) Predicted to enable signaling receptor binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.3084976).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITPRID1	NM_001257967.3	c.89C>A	p.Ala30Glu	missense_variant	Exon 3 of 15	ENST00000615280.5	NP_001244896.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITPRID1	ENST00000615280.5	c.89C>A	p.Ala30Glu	missense_variant	Exon 3 of 15	2	NM_001257967.3	ENSP00000478518.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.25
BayesDel_addAF	Benign	-0.096	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	6.3
DANN	Benign	0.91
DEOGEN2	Benign	0.019	.;.;.;.;T;.;.
Eigen	Benign	-0.52
Eigen_PC	Benign	-0.70
FATHMM_MKL	Benign	0.064	N
LIST_S2	Benign	0.68	T;T;T;T;T;T;T
M_CAP	Benign	0.032	D
MetaRNN	Benign	0.31	T;T;T;T;T;T;T
MetaSVM	Benign	-0.86	T
PrimateAI	Benign	0.27	T
PROVEAN	Uncertain	-4.2	.;D;D;N;N;D;D
REVEL	Benign	0.15
Sift	Uncertain	0.0060	.;D;D;D;D;D;D
Sift4G	Uncertain	0.041	D;D;D;T;D;D;D
Polyphen		0.99	.;.;.;D;D;.;.
Vest4		0.22
MutPred		0.21		.;Gain of ubiquitination at K25 (P = 0.0314);Gain of ubiquitination at K25 (P = 0.0314);Gain of ubiquitination at K25 (P = 0.0314);Gain of ubiquitination at K25 (P = 0.0314);.;Gain of ubiquitination at K25 (P = 0.0314);
MVP		0.61
MPC		0.21
ClinPred		0.97	D
GERP RS		2.6
Varity_R		0.30
gMVP		0.21

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs750792790; hg19: chr7-31592727;