rs3791809

chr2-190344992-C-T

Variant summary

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

The XM_047446773.1(LOC124906109):c.-676G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 152,068 control chromosomes in the GnomAD database, including 17,306 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 0.43 (17306 hom., cov: 33)
• Consequence: LOC124906109 XM_047446773.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462

Genes affected

LOC124906109 (HGNC:):

INPP1 (HGNC:6071): (inositol polyphosphate-1-phosphatase) This gene encodes the enzyme inositol polyphosphate-1-phosphatase, one of the enzymes involved in phosphatidylinositol signaling pathways. This enzyme removes the phosphate group at position 1 of the inositol ring from the polyphosphates inositol 1,4-bisphosphate and inositol 1,3,4-trisphophosphate. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124906109	XM_047446773.1	c.-676G>A		5_prime_UTR_variant	1/1
INPP1	NM_001128928.2	c.-209+1031C>T		intron_variant		ENST00000392329.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INPP1	ENST00000392329.7	c.-209+1031C>T		intron_variant		5	NM_001128928.2	P1

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65770 AN: 151948 Hom.: 17318 Cov.: 33

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.432 AC: 65745 AN: 152068 Hom.: 17306 Cov.: 33 AF XY: 0.431 AC XY: 32065 AN XY: 74328

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.469

Alfa AF: 0.556 Hom.: 12640

Bravo AF: 0.400

Asia WGS AF: 0.423 AC: 1476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	8.6
Dann	Benign	0.56

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: rs3791809; hg19: chr2-191209718;