17-10829555-A-G

Position:

• chr17-10829555-A-G

Variant summary

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

The NM_001101387.2(PIRT):​c.-138-3772T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 152,206 control chromosomes in the GnomAD database, including 61,757 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 0.90 (61757 hom., cov: 31)
• Consequence: PIRT NM_001101387.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

PIRT (HGNC:37239): (phosphoinositide interacting regulator of transient receptor potential channels) Predicted to enable phosphatidylinositol bisphosphate binding activity and transmembrane transporter binding activity. Predicted to be involved in phosphatidylinositol-mediated signaling and positive regulation of cation channel activity. Predicted to act upstream of or within behavioral response to pain and response to heat. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIRT	NM_001101387.2	c.-138-3772T>C		intron_variant		ENST00000580256.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIRT	ENST00000580256.3	c.-138-3772T>C		intron_variant		2	NM_001101387.2	P1

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136844 AN: 152088 Hom.: 61691 Cov.: 31

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.916

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.900 AC: 136970 AN: 152206 Hom.: 61757 Cov.: 31 AF XY: 0.902 AC XY: 67105 AN XY: 74424

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.935

Gnomad4 ASJ AF: 0.933

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.916

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.901

Alfa AF: 0.904 Hom.: 58209

Bravo AF: 0.904

Asia WGS AF: 0.920 AC: 3202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs9903961; hg19: chr17-10732872;