rs10495332

Variant summary

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

The NM_020808.5(SIPA1L2):​c.-319+9589A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0302 in 152,268 control chromosomes in the GnomAD database, including 378 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 0.030 ( 378 hom., cov: 33)

Consequence

SIPA1L2
NM_020808.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.02
Variant links:
Genes affected
SIPA1L2 (HGNC:23800): (signal induced proliferation associated 1 like 2) This gene encodes a member of the signal-induced proliferation-associated 1 like family. Members of this family contain a GTPase activating domain, a PDZ domain and a C-terminal coiled-coil domain with a leucine zipper. A similar protein in rat acts as a GTPases for the small GTPase Rap. [provided by RefSeq, Sep 2015]

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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SIPA1L2NM_020808.5 linkuse as main transcriptc.-319+9589A>G intron_variant ENST00000674635.1 NP_065859.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SIPA1L2ENST00000674635.1 linkuse as main transcriptc.-319+9589A>G intron_variant NM_020808.5 ENSP00000502693 A1Q9P2F8-1

Frequencies

GnomAD3 genomes
AF:
0.0303
AC:
4611
AN:
152148
Hom.:
381
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00673
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0208
Gnomad ASJ
AF:
0.0196
Gnomad EAS
AF:
0.353
Gnomad SAS
AF:
0.0375
Gnomad FIN
AF:
0.0331
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.0225
Gnomad OTH
AF:
0.0258
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0302
AC:
4603
AN:
152268
Hom.:
378
Cov.:
33
AF XY:
0.0323
AC XY:
2405
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.00671
Gnomad4 AMR
AF:
0.0210
Gnomad4 ASJ
AF:
0.0196
Gnomad4 EAS
AF:
0.353
Gnomad4 SAS
AF:
0.0365
Gnomad4 FIN
AF:
0.0331
Gnomad4 NFE
AF:
0.0225
Gnomad4 OTH
AF:
0.0241
Alfa
AF:
0.0207
Hom.:
17
Bravo
AF:
0.0309
Asia WGS
AF:
0.176
AC:
610
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.026
DANN
Benign
0.59

Splicing

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: rs10495332; hg19: chr1-232756026; API