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GeneBe

rs11597880

Positions:

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 0.282 in 151,982 control chromosomes in the GnomAD database, including 6,139 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 0.28 ( 6139 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.511
Variant links:

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ACMG classification

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=-0.81).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.282
AC:
42806
AN:
151864
Hom.:
6133
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.289
Gnomad AMI
AF:
0.301
Gnomad AMR
AF:
0.241
Gnomad ASJ
AF:
0.262
Gnomad EAS
AF:
0.206
Gnomad SAS
AF:
0.260
Gnomad FIN
AF:
0.240
Gnomad MID
AF:
0.222
Gnomad NFE
AF:
0.301
Gnomad OTH
AF:
0.295
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:
0.282
AC:
42828
AN:
151982
Hom.:
6139
Cov.:
31
AF XY:
0.279
AC XY:
20710
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.289
Gnomad4 AMR
AF:
0.241
Gnomad4 ASJ
AF:
0.262
Gnomad4 EAS
AF:
0.206
Gnomad4 SAS
AF:
0.259
Gnomad4 FIN
AF:
0.240
Gnomad4 NFE
AF:
0.301
Gnomad4 OTH
AF:
0.296
Alfa
AF:
0.287
Hom.:
769
Bravo
AF:
0.284
Asia WGS
AF:
0.252
AC:
879
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
2.8
DANN
Benign
0.68

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: rs11597880; hg19: chr10-126078272; API