rs10052280

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 0.115 in 149,738 control chromosomes in the GnomAD database, including 1,444 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 0.11 ( 1444 hom., cov: 27)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.207
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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.115
AC:
17183
AN:
149708
Hom.:
1437
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.222
Gnomad AMI
AF:
0.0859
Gnomad AMR
AF:
0.152
Gnomad ASJ
AF:
0.0707
Gnomad EAS
AF:
0.134
Gnomad SAS
AF:
0.0304
Gnomad FIN
AF:
0.0686
Gnomad MID
AF:
0.0523
Gnomad NFE
AF:
0.0559
Gnomad OTH
AF:
0.107
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.115
AC:
17212
AN:
149738
Hom.:
1444
Cov.:
27
AF XY:
0.116
AC XY:
8505
AN XY:
73054
show subpopulations
Gnomad4 AFR
AF:
0.222
Gnomad4 AMR
AF:
0.153
Gnomad4 ASJ
AF:
0.0707
Gnomad4 EAS
AF:
0.135
Gnomad4 SAS
AF:
0.0306
Gnomad4 FIN
AF:
0.0686
Gnomad4 NFE
AF:
0.0559
Gnomad4 OTH
AF:
0.107
Alfa
AF:
0.0664
Hom.:
879
Bravo
AF:
0.127
Asia WGS
AF:
0.100
AC:
347
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.6
DANN
Benign
0.66

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: rs10052280; hg19: chr5-83897084; API