rs12570088

Variant summary

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

The variant allele was found at a frequency of 0.043 in 152,204 control chromosomes in the GnomAD database, including 183 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 0.043 ( 183 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.797
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.0430
AC:
6535
AN:
152086
Hom.:
183
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0229
Gnomad AMI
AF:
0.0197
Gnomad AMR
AF:
0.0250
Gnomad ASJ
AF:
0.0744
Gnomad EAS
AF:
0.137
Gnomad SAS
AF:
0.102
Gnomad FIN
AF:
0.0526
Gnomad MID
AF:
0.0411
Gnomad NFE
AF:
0.0452
Gnomad OTH
AF:
0.0378
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0430
AC:
6539
AN:
152204
Hom.:
183
Cov.:
32
AF XY:
0.0453
AC XY:
3374
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.0230
Gnomad4 AMR
AF:
0.0250
Gnomad4 ASJ
AF:
0.0744
Gnomad4 EAS
AF:
0.137
Gnomad4 SAS
AF:
0.102
Gnomad4 FIN
AF:
0.0526
Gnomad4 NFE
AF:
0.0452
Gnomad4 OTH
AF:
0.0374
Alfa
AF:
0.0472
Hom.:
136
Bravo
AF:
0.0386
Asia WGS
AF:
0.0740
AC:
261
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
4.5
DANN
Benign
0.65

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: rs12570088; hg19: chr10-59938336; API