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GeneBe

5-95700996-C-T

Variant summary

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

The NM_001349303.2(SPATA9):c.-148+251G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,040 control chromosomes in the GnomAD database, including 24,778 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 0.57 ( 24778 hom., cov: 32)

Consequence

SPATA9
NM_001349303.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.222
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SPATA9NM_001349303.2 linkuse as main transcriptc.-148+251G>A intron_variant
SPATA9XM_047417809.1 linkuse as main transcriptc.-285+251G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.569
AC:
86412
AN:
151920
Hom.:
24746
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.591
Gnomad AMI
AF:
0.589
Gnomad AMR
AF:
0.524
Gnomad ASJ
AF:
0.451
Gnomad EAS
AF:
0.796
Gnomad SAS
AF:
0.605
Gnomad FIN
AF:
0.644
Gnomad MID
AF:
0.427
Gnomad NFE
AF:
0.540
Gnomad OTH
AF:
0.551
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.569
AC:
86495
AN:
152040
Hom.:
24778
Cov.:
32
AF XY:
0.575
AC XY:
42705
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.591
Gnomad4 AMR
AF:
0.525
Gnomad4 ASJ
AF:
0.451
Gnomad4 EAS
AF:
0.797
Gnomad4 SAS
AF:
0.605
Gnomad4 FIN
AF:
0.644
Gnomad4 NFE
AF:
0.540
Gnomad4 OTH
AF:
0.557
Alfa
AF:
0.542
Hom.:
25116
Bravo
AF:
0.563
Asia WGS
AF:
0.665
AC:
2309
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
Cadd
Benign
2.2
Dann
Benign
0.77

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: rs153916; hg19: chr5-95036700; API