rs2191343

Positions:

• chr7-31599316-A-G
• chr7-31599316-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001257967.3(ITPRID1):​c.1228+16125A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,978 control chromosomes in the GnomAD database, including 18,533 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (18533 hom., cov: 32)
• Consequence: ITPRID1 NM_001257967.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITPRID1	NM_001257967.3	c.1228+16125A>G		intron_variant		ENST00000615280.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ITPRID1	ENST00000615280.5	c.1228+16125A>G		intron_variant		2	NM_001257967.3	P2
ITPRID1	ENST00000407970.7	c.1228+16125A>G		intron_variant		1		P2
ITPRID1	ENST00000319386.7	c.784+16125A>G		intron_variant		2
ITPRID1	ENST00000409210.1	c.952+16125A>G		intron_variant		2		A2

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73439 AN: 151860 Hom.: 18511 Cov.: 32

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.468

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.484 AC: 73492 AN: 151978 Hom.: 18533 Cov.: 32 AF XY: 0.481 AC XY: 35692 AN XY: 74270

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.470

Alfa AF: 0.453 Hom.: 2012

Bravo AF: 0.505

Asia WGS AF: 0.428 AC: 1484 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.9
DANN	Benign	0.87

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: rs2191343; hg19: chr7-31638930;