rs1320251313

Variant names:

• chr7-31553142-C-A
• NM_001257967.3:c.118C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-31553142-C-A
• chr7-31553142-C-G
• chr7-31553142-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001257967.3(ITPRID1):​c.118C>A​(p.Pro40Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000694 in 1,440,160 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 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)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: ITPRID1 NM_001257967.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.588

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 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.19763276).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITPRID1	NM_001257967.3	c.118C>A	p.Pro40Thr	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.118C>A	p.Pro40Thr	missense_variant	Exon 3 of 15	2	NM_001257967.3	ENSP00000478518.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.94e-7 AC: 1 AN: 1440160 Hom.: 0 Cov.: 33 AF XY: 0.00000140 AC XY: 1 AN XY: 714046

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000121

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.072
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Benign	17
DANN	Uncertain	0.98
DEOGEN2	Benign	0.0034	.;.;.;.;T;.;.
Eigen	Benign	-0.11
Eigen_PC	Benign	-0.28
FATHMM_MKL	Benign	0.079	N
LIST_S2	Benign	0.76	T;T;T;T;T;T;T
M_CAP	Benign	0.010	T
MetaRNN	Benign	0.20	T;T;T;T;T;T;T
MetaSVM	Benign	-0.91	T
PrimateAI	Benign	0.28	T
PROVEAN	Pathogenic	-6.2	.;D;D;N;N;N;D
REVEL	Benign	0.099
Sift	Uncertain	0.0090	.;D;D;D;D;D;D
Sift4G	Uncertain	0.016	D;D;D;D;D;D;D
Polyphen		0.98	.;.;.;D;D;.;.
Vest4		0.16
MutPred		0.28		.;Loss of catalytic residue at P40 (P = 0.0083);Loss of catalytic residue at P40 (P = 0.0083);Loss of catalytic residue at P40 (P = 0.0083);Loss of catalytic residue at P40 (P = 0.0083);.;Loss of catalytic residue at P40 (P = 0.0083);
MVP		0.33
MPC		0.21
ClinPred		0.66	D
GERP RS		4.3
Varity_R		0.080
gMVP		0.070

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-31592756;