7-31584132-T-C

Variant names:

• chr7-31584132-T-C
• rs1014137
• NM_001257967.3:c.1228+941T>C

Variant summary

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

The NM_001257967.3(ITPRID1):​c.1228+941T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,016 control chromosomes in the GnomAD database, including 18,939 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 0.49 (18939 hom., cov: 32)
• Consequence: ITPRID1 NM_001257967.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITPRID1	NM_001257967.3	c.1228+941T>C		intron_variant	Intron 10 of 14	ENST00000615280.5	NP_001244896.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITPRID1	ENST00000615280.5	c.1228+941T>C		intron_variant	Intron 10 of 14	2	NM_001257967.3	ENSP00000478518.2
ITPRID1	ENST00000407970.7	c.1228+941T>C		intron_variant	Intron 9 of 13	1		ENSP00000384416.3
ITPRID1	ENST00000409210.1	c.952+941T>C		intron_variant	Intron 7 of 12	2		ENSP00000387214.1
ITPRID1	ENST00000319386.7	c.784+941T>C		intron_variant	Intron 9 of 13	2		ENSP00000313062.3

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73978 AN: 151898 Hom.: 18911 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.487 AC: 74045 AN: 152016 Hom.: 18939 Cov.: 32 AF XY: 0.484 AC XY: 35931 AN XY: 74290

African (AFR) AF: 0.637 AC: 26387 AN: 41446

American (AMR) AF: 0.534 AC: 8157 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1206 AN: 3468

East Asian (EAS) AF: 0.466 AC: 2402 AN: 5160

South Asian (SAS) AF: 0.446 AC: 2152 AN: 4822

European-Finnish (FIN) AF: 0.370 AC: 3916 AN: 10570

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28450 AN: 67972

Other (OTH) AF: 0.466 AC: 984 AN: 2112

Alfa AF: 0.439 Hom.: 61972

Bravo AF: 0.509

Asia WGS AF: 0.423 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.69
DANN	Benign	0.52
PhyloP100		-0.26
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: rs1014137; hg19: chr7-31623746;