rs61199332
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The variant allele was found at a frequency of 0.0602 in 152,304 control chromosomes in the GnomAD database, including 563 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.060 ( 563 hom., cov: 33)
Consequence
Unknown
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0330
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 8-11573132-C-T is Benign according to our data. Variant chr8-11573132-C-T is described in ClinVar as [Benign]. Clinvar id is 12321.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|
Frequencies
GnomAD3 genomes ? AF: 0.0600 AC: 9134AN: 152186Hom.: 555 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
9134
AN:
152186
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: 0.0602 AC: 9168AN: 152304Hom.: 563 Cov.: 33 AF XY: 0.0591 AC XY: 4402AN XY: 74478
GnomAD4 genome
?
AF:
AC:
9168
AN:
152304
Hom.:
Cov.:
33
AF XY:
AC XY:
4402
AN XY:
74478
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
134
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Pathogenic:1Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Maturity-onset diabetes of the young type 11 Pathogenic:1Benign:1
Benign, no assertion criteria provided | curation | Reproductive Health Research and Development, BGI Genomics | Jan 06, 2020 | NC_000008.11:g.11573132C>T has an allele frequency of 0.163 in African subpopulation in the gnomAD database, including 128 homozygous occurrences. This variant was annotated at the position 11,468,050 on chromsome 8. In the functional study by MIN6 beta-cells, this variant decreased luciferase expression as compared with control constructs without any insert (PMID: 19667185). This evidence suggests the variant to be classified as benign. ACMG/AMP criteria applied: BA1, BS2, PS3. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 25, 2009 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | research | H3Africa Consortium | Oct 28, 2020 | While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.146, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error. - |
BLK-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 12, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at