rs2020932

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 0.131 in 151,626 control chromosomes in the GnomAD database, including 2,729 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 0.13 ( 2729 hom., cov: 31)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.138
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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 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:
0.130
AC:
19764
AN:
151510
Hom.:
2713
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.347
Gnomad AMI
AF:
0.00329
Gnomad AMR
AF:
0.0723
Gnomad ASJ
AF:
0.0934
Gnomad EAS
AF:
0.0510
Gnomad SAS
AF:
0.101
Gnomad FIN
AF:
0.0246
Gnomad MID
AF:
0.0918
Gnomad NFE
AF:
0.0418
Gnomad OTH
AF:
0.116
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.131
AC:
19818
AN:
151626
Hom.:
2729
Cov.:
31
AF XY:
0.129
AC XY:
9537
AN XY:
74096
show subpopulations
Gnomad4 AFR
AF:
0.347
Gnomad4 AMR
AF:
0.0720
Gnomad4 ASJ
AF:
0.0934
Gnomad4 EAS
AF:
0.0501
Gnomad4 SAS
AF:
0.100
Gnomad4 FIN
AF:
0.0246
Gnomad4 NFE
AF:
0.0418
Gnomad4 OTH
AF:
0.115
Alfa
AF:
0.0933
Hom.:
207
Bravo
AF:
0.142
Asia WGS
AF:
0.0950
AC:
331
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.7
DANN
Benign
0.58

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: rs2020932; hg19: chr17-28563499; API