10-132746836-A-G

Variant names:

• chr10-132746836-A-G
• rs2803990
• NM_005539.5:c.733-2681A>G

Variant summary

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

The NM_005539.5(INPP5A):​c.733-2681A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,208 control chromosomes in the GnomAD database, including 5,203 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 0.26 (5203 hom., cov: 34)
• Consequence: INPP5A NM_005539.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440
• Publications: 1 publications found

Genes affected

INPP5A (HGNC:6076): (inositol polyphosphate-5-phosphatase A) The protein encoded by this gene is a membrane-associated type I inositol 1,4,5-trisphosphate (InsP3) 5-phosphatase. InsP3 5-phosphatases hydrolyze Ins(1,4,5)P3, which mobilizes intracellular calcium and acts as a second messenger mediating cell responses to various stimulation. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005539.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INPP5A	NM_005539.5	MANE Select	c.733-2681A>G		intron	N/A	NP_005530.3
	INPP5A	NM_001321042.2		c.541-2681A>G		intron	N/A	NP_001307971.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INPP5A	ENST00000368594.8	TSL:1 MANE Select	c.733-2681A>G		intron	N/A	ENSP00000357583.3
	INPP5A	ENST00000368593.7	TSL:1	c.733-2681A>G		intron	N/A	ENSP00000357582.3
	INPP5A	ENST00000342652.6	TSL:5	c.646-18937A>G		intron	N/A	ENSP00000340707.6

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39199 AN: 152090 Hom.: 5197 Cov.: 34

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.258 AC: 39243 AN: 152208 Hom.: 5203 Cov.: 34 AF XY: 0.254 AC XY: 18933 AN XY: 74440

African (AFR) AF: 0.274 AC: 11364 AN: 41528

American (AMR) AF: 0.219 AC: 3354 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 865 AN: 3470

East Asian (EAS) AF: 0.131 AC: 679 AN: 5186

South Asian (SAS) AF: 0.259 AC: 1250 AN: 4822

European-Finnish (FIN) AF: 0.235 AC: 2493 AN: 10592

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18503 AN: 68000

Other (OTH) AF: 0.257 AC: 541 AN: 2108

Alfa AF: 0.267 Hom.: 913

Bravo AF: 0.256

Asia WGS AF: 0.226 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	2.8
DANN	Benign	0.63
PhyloP100		-0.44
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: rs2803990; hg19: chr10-134560340;