rs217170

Variant names:

• chr7-31525103-A-G
• rs217170
• NM_001257967.3:c.-98+10983A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001257967.3(ITPRID1):​c.-98+10983A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,160 control chromosomes in the GnomAD database, including 3,138 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 0.17 (3138 hom., cov: 32)
• Consequence: ITPRID1 NM_001257967.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001257967.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITPRID1	NM_001257967.3	MANE Select	c.-98+10983A>G		intron	N/A	NP_001244896.2
	ITPRID1	NR_047565.3		n.757+6766A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ITPRID1	ENST00000615280.5	TSL:2 MANE Select	c.-98+10983A>G		intron	N/A	ENSP00000478518.2
	ITPRID1	ENST00000407970.7	TSL:1	c.-20+6766A>G		intron	N/A	ENSP00000384416.3
	ITPRID1	ENST00000888409.1		c.-20+10898A>G		intron	N/A	ENSP00000558468.1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26246 AN: 152042 Hom.: 3125 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.0978

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.0720

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.173 AC: 26315 AN: 152160 Hom.: 3138 Cov.: 32 AF XY: 0.176 AC XY: 13070 AN XY: 74412

African (AFR) AF: 0.308 AC: 12778 AN: 41478

American (AMR) AF: 0.255 AC: 3889 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0978 AC: 339 AN: 3466

East Asian (EAS) AF: 0.208 AC: 1080 AN: 5182

South Asian (SAS) AF: 0.231 AC: 1113 AN: 4814

European-Finnish (FIN) AF: 0.0720 AC: 764 AN: 10610

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0872 AC: 5930 AN: 68012

Other (OTH) AF: 0.172 AC: 364 AN: 2116

Alfa AF: 0.147 Hom.: 445

Bravo AF: 0.193

Asia WGS AF: 0.216 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.4
DANN	Benign	0.79
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs217170; hg19: chr7-31564717;