rs2803990

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.440
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
INPP5ANM_005539.5 linkuse as main transcriptc.733-2681A>G intron_variant ENST00000368594.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
INPP5AENST00000368594.8 linkuse as main transcriptc.733-2681A>G intron_variant 1 NM_005539.5 P1
INPP5AENST00000368593.7 linkuse as main transcriptc.733-2681A>G intron_variant 1
INPP5AENST00000342652.6 linkuse as main transcriptc.647-18937A>G intron_variant 5
INPP5AENST00000498337.1 linkuse as main transcriptn.195-2681A>G intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.258
AC:
39199
AN:
152090
Hom.:
5197
Cov.:
34
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.274
Gnomad4 AMR
AF:
0.219
Gnomad4 ASJ
AF:
0.249
Gnomad4 EAS
AF:
0.131
Gnomad4 SAS
AF:
0.259
Gnomad4 FIN
AF:
0.235
Gnomad4 NFE
AF:
0.272
Gnomad4 OTH
AF:
0.257
Alfa
AF:
0.267
Hom.:
883
Bravo
AF:
0.256
Asia WGS
AF:
0.226
AC:
789
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
2.8
DANN
Benign
0.63

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2803990; hg19: chr10-134560340; API