chr2-96327946-G-A

Position:

• chr2-96327946-G-A

Variant summary

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

The NM_001008949.3(ITPRIPL1):​c.1315G>A​(p.Ala439Thr) 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. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ITPRIPL1 NM_001008949.3 missense
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 1.65

Genes affected

ITPRIPL1 (HGNC:29371): (ITPRIP like 1) Located in membrane. [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=0.082819134).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITPRIPL1	NM_001008949.3	c.1315G>A	p.Ala439Thr	missense_variant	3/3	ENST00000439118.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITPRIPL1	ENST00000439118.3	c.1315G>A	p.Ala439Thr	missense_variant	3/3	1	NM_001008949.3
ITPRIPL1	ENST00000420728.1	c.1411G>A	p.Ala471Thr	missense_variant	2/2	2
ITPRIPL1	ENST00000361124.5	c.1339G>A	p.Ala447Thr	missense_variant	1/1
ITPRIPL1	ENST00000536814.1	c.1291G>A	p.Ala431Thr	missense_variant	2/2	3		P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

Malignant tumor of prostate Uncertain:1

Uncertain significance, no assertion criteria provided

literature only

Science for Life laboratory, Karolinska Institutet

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.069
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	15
DANN	Benign	0.97
DEOGEN2	Benign	0.0014	.;T;.
Eigen	Benign	-0.29
Eigen_PC	Benign	-0.24
FATHMM_MKL	Benign	0.46	N
LIST_S2	Benign	0.79	T;T;T
M_CAP	Benign	0.0068	T
MetaRNN	Benign	0.083	T;T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	1.5	.;L;.
MutationTaster	Benign	1.0	N;N;N;N
PrimateAI	Benign	0.31	T
PROVEAN	Benign	0.080	N;N;N
REVEL	Benign	0.035
Sift	Benign	0.069	T;T;T
Sift4G	Benign	0.23	T;T;T
Polyphen		0.46, 0.40	.;P;B
Vest4		0.25
MutPred		0.20		.;Gain of glycosylation at A439 (P = 0.0297);.;
MVP		0.24
MPC		0.22
ClinPred		0.10	T
GERP RS		2.4
Varity_R		0.034
gMVP		0.093

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

LitVar

Other links and lift over

dbSNP: rs193921120; hg19: chr2-96993684; COSMIC: COSV63152933; COSMIC: COSV63152933;