rs10486661
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The variant allele was found at a frequency of 0.138 in 152,274 control chromosomes in the GnomAD database, including 1,617 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 0.14 ( 1617 hom., cov: 33)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.22
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ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 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 |
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Frequencies
GnomAD3 genomes AF: 0.138 AC: 20966AN: 152156Hom.: 1616 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
20966
AN:
152156
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.138 AC: 20975AN: 152274Hom.: 1617 Cov.: 33 AF XY: 0.133 AC XY: 9927AN XY: 74474 show subpopulations
GnomAD4 genome
AF:
AC:
20975
AN:
152274
Hom.:
Cov.:
33
AF XY:
AC XY:
9927
AN XY:
74474
Gnomad4 AFR
AF:
AC:
0.100597
AN:
0.100597
Gnomad4 AMR
AF:
AC:
0.137178
AN:
0.137178
Gnomad4 ASJ
AF:
AC:
0.27813
AN:
0.27813
Gnomad4 EAS
AF:
AC:
0.107294
AN:
0.107294
Gnomad4 SAS
AF:
AC:
0.161899
AN:
0.161899
Gnomad4 FIN
AF:
AC:
0.0608172
AN:
0.0608172
Gnomad4 NFE
AF:
AC:
0.163893
AN:
0.163893
Gnomad4 OTH
AF:
AC:
0.182464
AN:
0.182464
Heterozygous variant carriers
0
929
1858
2787
3716
4645
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
246
492
738
984
1230
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
455
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at